Starting phenix.real_space_refine on Sat Mar 7 06:25:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r0z_4702/03_2026/6r0z_4702.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r0z_4702/03_2026/6r0z_4702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r0z_4702/03_2026/6r0z_4702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r0z_4702/03_2026/6r0z_4702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r0z_4702/03_2026/6r0z_4702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r0z_4702/03_2026/6r0z_4702.map" } resolution = 3.8 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= 0.018 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 103 5.16 5 C 25043 2.51 5 N 7295 2.21 5 O 7738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.04s 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: 40184 Number of models: 1 Model: "" Number of chains: 27 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: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} 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: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3616 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 435} Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3608 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 434} Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1647 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} 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: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 809 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "L" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 3185 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 517} Link IDs: {'PTRANS': 36, 'TRANS': 611} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2027 Unresolved non-hydrogen angles: 2625 Unresolved non-hydrogen dihedrals: 1711 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.10, per 1000 atoms: 0.23 Number of scatterers: 40184 At special positions: 0 Unit cell: (146.475, 147.56, 259.315, 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 103 16.00 P 4 15.00 Mg 1 11.99 O 7738 8.00 N 7295 7.00 C 25043 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: 3.39 Conformation dependent library (CDL) restraints added in 2.1 seconds 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10538 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 39 sheets defined 56.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.617A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.841A pdb=" N GLY A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.764A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.603A pdb=" N TYR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.256A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 4.078A pdb=" N SER A 433 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 434 " --> pdb=" O PHE A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 471 removed outlier: 4.677A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 533 removed outlier: 3.656A pdb=" N ALA A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 558 through 573 removed outlier: 3.596A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.573A pdb=" N LEU B 272 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.801A 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 316 removed outlier: 3.599A pdb=" N ARG B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 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: 4.314A 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 472 removed outlier: 3.642A pdb=" N LEU B 450 " --> pdb=" O ASP B 446 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 494 Processing helix chain 'B' and resid 508 through 533 removed outlier: 4.422A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.753A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 540 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 535 through 541' Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 559 through 577 removed outlier: 4.199A pdb=" N GLU B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.031A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.088A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.589A 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 393 through 401 removed outlier: 3.747A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) 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: 4.603A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) 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 508 through 531 Processing helix chain 'C' and resid 535 through 540 removed outlier: 3.675A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 540 " --> pdb=" O ILE C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 540' Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 558 through 573 removed outlier: 3.898A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.868A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.892A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 removed outlier: 4.007A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) 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: 3.692A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.745A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.766A pdb=" N HIS D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 397 removed outlier: 4.023A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG D 393 " --> pdb=" O GLY D 389 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 422 removed outlier: 4.321A pdb=" N ARG D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.518A pdb=" N SER D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.673A 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 removed outlier: 4.310A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 249 removed outlier: 3.749A 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 259 through 272 removed outlier: 3.909A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 293 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 341 through 346 removed outlier: 3.626A pdb=" N LYS E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.509A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 397 Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.744A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 455 through 462 removed outlier: 3.507A 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 171 removed outlier: 3.600A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 212 Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 232 through 248 removed outlier: 4.467A pdb=" N ARG F 236 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL F 241 " --> pdb=" O MET F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 removed outlier: 4.116A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) 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 347 removed outlier: 3.672A pdb=" N HIS F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.682A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 422 removed outlier: 3.572A pdb=" N TYR F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 412 " --> pdb=" O ASP F 408 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 463 removed outlier: 3.896A pdb=" N TYR F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.637A pdb=" N LEU G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.192A pdb=" N VAL G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 169 removed outlier: 3.561A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 211 removed outlier: 3.741A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 16 removed outlier: 3.899A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 55 through 63 removed outlier: 3.905A pdb=" N VAL H 59 " --> pdb=" O PRO H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 19 through 103 Processing helix chain 'I' and resid 106 through 116 removed outlier: 3.756A pdb=" N ALA I 112 " --> pdb=" O ASP I 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 94 removed outlier: 3.999A pdb=" N GLU J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 100 through 114 removed outlier: 3.960A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (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 166 through 187 removed outlier: 5.487A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 107 removed outlier: 3.629A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 119 removed outlier: 4.080A pdb=" N ALA K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 93 removed outlier: 3.677A pdb=" N GLU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG L 47 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU L 80 " --> pdb=" O ARG L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 3.566A pdb=" N LEU L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 132 removed outlier: 3.667A pdb=" N LEU L 131 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 128 through 132' Processing helix chain 'L' and resid 133 through 137 removed outlier: 3.601A pdb=" N ARG L 136 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 187 removed outlier: 5.628A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU L 178 " --> pdb=" O ALA L 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 18 removed outlier: 3.829A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 28 removed outlier: 3.601A 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 49 removed outlier: 3.906A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU M 48 " --> pdb=" O TYR M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 70 Processing helix chain 'M' and resid 78 through 86 removed outlier: 3.797A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 106 Processing helix chain 'M' and resid 120 through 127 Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 145 through 155 removed outlier: 4.045A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 182 Processing helix chain 'M' and resid 187 through 207 Processing helix chain 'M' and resid 213 through 218 removed outlier: 3.746A pdb=" N PHE M 217 " --> pdb=" O ALA M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 237 through 243 removed outlier: 4.084A pdb=" N LEU M 241 " --> pdb=" O ASP M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 275 Processing helix chain 'M' and resid 276 through 278 No H-bonds generated for 'chain 'M' and resid 276 through 278' Processing helix chain 'M' and resid 283 through 310 Processing helix chain 'M' and resid 316 through 320 removed outlier: 3.789A pdb=" N VAL M 320 " --> pdb=" O GLU M 317 " (cutoff:3.500A) 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: 3.853A pdb=" N TYR N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 129 removed outlier: 3.641A pdb=" N LEU N 122 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 160 removed outlier: 3.823A pdb=" N VAL N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 197 Processing helix chain 'N' and resid 212 through 267 Proline residue: N 228 - end of helix removed outlier: 5.768A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU N 267 " --> pdb=" O LEU N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 285 No H-bonds generated for 'chain 'N' and resid 283 through 285' Processing helix chain 'N' and resid 286 through 295 Processing helix chain 'N' and resid 327 through 329 No H-bonds generated for 'chain 'N' and resid 327 through 329' Processing helix chain 'N' and resid 330 through 335 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: 3.986A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 489 Processing helix chain 'N' and resid 491 through 516 removed outlier: 3.522A pdb=" N PHE N 495 " --> pdb=" O HIS N 491 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 543 Processing helix chain 'N' and resid 547 through 560 Processing helix chain 'N' and resid 561 through 588 removed outlier: 4.359A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 593 through 632 removed outlier: 5.239A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 4.059A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE N 632 " --> pdb=" O PHE N 628 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 3.792A pdb=" N GLY O 13 " --> pdb=" O GLY O 9 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 4.193A 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: 4.249A 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 62 through 79 removed outlier: 4.150A pdb=" N VAL P 66 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 48 removed outlier: 4.053A 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 62 through 79 removed outlier: 4.268A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 48 removed outlier: 4.125A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 removed outlier: 3.702A pdb=" N ILE R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.473A pdb=" N VAL R 66 " --> pdb=" O PRO R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 48 removed outlier: 4.195A 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 11 through 48 removed outlier: 3.611A pdb=" N ILE T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.750A 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 62 through 80 removed outlier: 4.210A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 48 removed outlier: 4.125A 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 62 through 80 removed outlier: 4.140A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 48 removed outlier: 4.129A pdb=" N GLY V 13 " --> pdb=" O GLY V 9 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.682A 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 63 through 79 Processing helix chain 'W' and resid 11 through 48 removed outlier: 4.074A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 62 through 80 removed outlier: 4.492A pdb=" N VAL W 66 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 48 removed outlier: 4.095A pdb=" N LEU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.759A pdb=" N ALA X 55 " --> pdb=" O ASN X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 80 removed outlier: 4.449A pdb=" N VAL X 66 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 48 removed outlier: 4.032A 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: 3.807A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 4.095A 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 'A' and resid 3 through 9 removed outlier: 6.555A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.401A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR A 291 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.401A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR A 291 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 224 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.922A pdb=" N ILE A 147 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 40 removed outlier: 5.664A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR D 13 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU D 22 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE D 11 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 64 Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.644A pdb=" N ILE E 14 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE E 11 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU E 22 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL E 50 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.320A pdb=" N GLY B 82 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA B 289 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR B 84 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB4, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.789A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 137 through 139 Processing sheet with id=AB6, first strand: chain 'B' and resid 197 through 198 removed outlier: 3.939A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 10 removed outlier: 6.659A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.596A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL F 50 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU F 75 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS F 6 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU L 121 " --> pdb=" O GLN L 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.207A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP C 325 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 253 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.207A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP C 325 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 253 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 224 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 145 through 148 removed outlier: 4.283A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 128 through 129 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 94 removed outlier: 8.777A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 188 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE D 256 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL D 190 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 258 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA D 192 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL D 308 " --> pdb=" O GLY D 299 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 92 through 94 removed outlier: 8.777A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 188 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE D 256 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL D 190 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 258 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA D 192 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE D 152 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 7 through 8 removed outlier: 6.396A pdb=" N LEU J 121 " --> pdb=" O GLN J 143 " (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 131 through 132 Processing sheet with id=AD3, first strand: chain 'E' and resid 217 through 219 removed outlier: 4.109A pdb=" N ALA E 188 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL E 253 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE E 311 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL E 255 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE E 313 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU E 257 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N SER E 315 " --> pdb=" O LEU E 257 " (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 92 through 93 removed outlier: 6.703A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE F 313 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU F 257 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N SER F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE F 152 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.466A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 90 through 96 Processing sheet with id=AD8, first strand: chain 'H' and resid 2 through 4 removed outlier: 6.827A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 31 through 33 removed outlier: 4.371A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA N 270 " --> pdb=" O ALA N 277 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 31 through 33 removed outlier: 4.371A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 140 through 145 Processing sheet with id=AE3, first strand: chain 'N' and resid 389 through 391 2671 hydrogen bonds defined for protein. 7803 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: 9.76 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10592 1.33 - 1.45: 6507 1.45 - 1.57: 23424 1.57 - 1.69: 8 1.69 - 1.80: 194 Bond restraints: 40725 Sorted by residual: bond pdb=" C LEU J 94 " pdb=" N PRO J 95 " ideal model delta sigma weight residual 1.335 1.386 -0.051 1.38e-02 5.25e+03 1.36e+01 bond pdb=" C LEU L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.21e+00 bond pdb=" CB ASP B 152 " pdb=" CG ASP B 152 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.88e+00 bond pdb=" CG LEU C 322 " pdb=" CD1 LEU C 322 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.95e+00 bond pdb=" CA ASP H 85 " pdb=" CB ASP H 85 " ideal model delta sigma weight residual 1.527 1.559 -0.032 1.61e-02 3.86e+03 3.86e+00 ... (remaining 40720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 54559 3.22 - 6.44: 687 6.44 - 9.66: 101 9.66 - 12.88: 16 12.88 - 16.11: 3 Bond angle restraints: 55366 Sorted by residual: angle pdb=" N VAL B 265 " pdb=" CA VAL B 265 " pdb=" C VAL B 265 " ideal model delta sigma weight residual 112.96 106.23 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" N GLY A 366 " pdb=" CA GLY A 366 " pdb=" C GLY A 366 " ideal model delta sigma weight residual 113.18 128.17 -14.99 2.37e+00 1.78e-01 4.00e+01 angle pdb=" C PRO B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta sigma weight residual 124.82 134.57 -9.75 1.78e+00 3.16e-01 3.00e+01 angle pdb=" C GLU E 22 " pdb=" N ASN E 23 " pdb=" CA ASN E 23 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.68e+01 angle pdb=" CA ASP H 85 " pdb=" CB ASP H 85 " pdb=" CG ASP H 85 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 ... (remaining 55361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 24168 29.56 - 59.11: 309 59.11 - 88.67: 5 88.67 - 118.22: 1 118.22 - 147.78: 1 Dihedral angle restraints: 24484 sinusoidal: 7993 harmonic: 16491 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 87.78 -147.78 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" CA MET A 294 " pdb=" C MET A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA GLU F 182 " pdb=" C GLU F 182 " pdb=" N LYS F 183 " pdb=" CA LYS F 183 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 24481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5619 0.084 - 0.168: 745 0.168 - 0.252: 49 0.252 - 0.337: 4 0.337 - 0.421: 2 Chirality restraints: 6419 Sorted by residual: 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 2.22 0.42 2.00e-01 2.50e+01 4.42e+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 -2.22 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA ASP F 259 " pdb=" N ASP F 259 " pdb=" C ASP F 259 " pdb=" CB ASP F 259 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 6416 not shown) Planarity restraints: 7462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 234 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LYS C 234 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS C 234 " -0.022 2.00e-02 2.50e+03 pdb=" N THR C 235 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 198 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C GLN F 198 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN F 198 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG F 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 226 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO C 227 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 227 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 227 " 0.039 5.00e-02 4.00e+02 ... (remaining 7459 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1210 2.70 - 3.25: 38293 3.25 - 3.80: 64180 3.80 - 4.35: 75889 4.35 - 4.90: 130463 Nonbonded interactions: 310035 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.152 2.170 nonbonded pdb=" OE2 GLU D 109 " pdb=" OH TYR D 244 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASP B 446 " pdb=" OH TYR B 513 " model vdw 2.276 3.040 nonbonded pdb=" O PRO C 386 " pdb=" OH TYR E 331 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLU A 38 " pdb=" OH TYR A 52 " model vdw 2.278 3.040 ... (remaining 310030 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' and resid 1 through 577) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 5 through 464) 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' } 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: 0.180 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: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 38.790 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 0.091 40725 Z= 0.293 Angle : 0.973 16.106 55366 Z= 0.526 Chirality : 0.057 0.421 6419 Planarity : 0.007 0.071 7462 Dihedral : 9.782 147.776 13946 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 0.19 % Allowed : 4.41 % Favored : 95.40 % Cbeta Deviations : 0.02 % 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: -3.88 (0.08), residues: 5795 helix: -2.14 (0.06), residues: 3121 sheet: -2.46 (0.19), residues: 600 loop : -3.07 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 401 TYR 0.029 0.003 TYR D 411 PHE 0.031 0.003 PHE D 204 TRP 0.036 0.003 TRP A 438 HIS 0.009 0.003 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00682 (40725) covalent geometry : angle 0.97301 (55366) hydrogen bonds : bond 0.09756 ( 2649) hydrogen bonds : angle 5.83668 ( 7803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1050 time to evaluate : 1.404 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 TARDY: cannot create tardy model for: "PRO L 146 " (corrupted residue). Skipping it. Corrupt residue: chain: L residue: PRO 146 >>> skipping REVERT: A 26 ASP cc_start: 0.9174 (m-30) cc_final: 0.8613 (m-30) REVERT: A 33 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8049 (tp30) REVERT: A 69 LEU cc_start: 0.8848 (mp) cc_final: 0.8535 (mt) REVERT: A 156 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7799 (mtp85) REVERT: A 246 ASN cc_start: 0.8621 (p0) cc_final: 0.8339 (p0) REVERT: A 282 MET cc_start: 0.9080 (tpt) cc_final: 0.8697 (tpt) REVERT: A 294 MET cc_start: 0.9217 (mtp) cc_final: 0.8646 (mtp) REVERT: A 319 SER cc_start: 0.9215 (t) cc_final: 0.9001 (p) REVERT: A 343 GLU cc_start: 0.8585 (pp20) cc_final: 0.8334 (mt-10) REVERT: A 452 ASP cc_start: 0.8873 (m-30) cc_final: 0.8297 (t0) REVERT: A 474 ASP cc_start: 0.8002 (t70) cc_final: 0.7471 (p0) REVERT: B 29 LYS cc_start: 0.8974 (mptp) cc_final: 0.8677 (mmtm) REVERT: B 274 ASP cc_start: 0.8299 (t0) cc_final: 0.7224 (p0) REVERT: B 276 LYS cc_start: 0.9126 (tptp) cc_final: 0.8325 (mtmt) REVERT: B 282 MET cc_start: 0.9075 (mmm) cc_final: 0.8872 (mmt) REVERT: B 401 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8199 (tpt170) REVERT: B 436 ASP cc_start: 0.8922 (m-30) cc_final: 0.8612 (m-30) REVERT: B 465 GLN cc_start: 0.8883 (tt0) cc_final: 0.8668 (mm-40) REVERT: B 477 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7249 (mp10) REVERT: B 478 ASP cc_start: 0.9094 (m-30) cc_final: 0.8841 (m-30) REVERT: B 500 TYR cc_start: 0.8684 (m-80) cc_final: 0.8329 (m-80) REVERT: B 525 GLU cc_start: 0.8749 (tp30) cc_final: 0.8536 (tp30) REVERT: C 154 ARG cc_start: 0.9277 (pmm150) cc_final: 0.8991 (ptp90) REVERT: C 332 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8857 (tt0) REVERT: C 340 ARG cc_start: 0.9467 (tpp-160) cc_final: 0.9164 (tpp80) REVERT: C 363 GLU cc_start: 0.9284 (tp30) cc_final: 0.9002 (tp30) REVERT: C 392 SER cc_start: 0.9143 (p) cc_final: 0.8750 (p) REVERT: C 461 GLU cc_start: 0.9349 (tm-30) cc_final: 0.9078 (tm-30) REVERT: C 493 ASP cc_start: 0.9256 (t0) cc_final: 0.8889 (t0) REVERT: C 525 GLU cc_start: 0.8269 (tt0) cc_final: 0.7893 (tt0) REVERT: C 550 ARG cc_start: 0.9042 (ppp-140) cc_final: 0.8686 (ttp80) REVERT: C 570 ILE cc_start: 0.9034 (mm) cc_final: 0.8827 (mm) REVERT: D 128 GLU cc_start: 0.8678 (pt0) cc_final: 0.8069 (tm-30) REVERT: D 185 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8297 (mm-30) REVERT: D 207 GLU cc_start: 0.9069 (tt0) cc_final: 0.8840 (tp30) REVERT: D 210 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8299 (ttp80) REVERT: D 318 ASP cc_start: 0.8526 (t70) cc_final: 0.8206 (t70) REVERT: D 327 ASP cc_start: 0.9172 (t0) cc_final: 0.8930 (t0) REVERT: D 380 ASP cc_start: 0.8788 (t0) cc_final: 0.8227 (t0) REVERT: D 381 GLN cc_start: 0.9193 (tp40) cc_final: 0.8948 (tp40) REVERT: D 398 ILE cc_start: 0.9344 (pt) cc_final: 0.8954 (mt) REVERT: E 162 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8626 (mp0) REVERT: E 176 ASP cc_start: 0.8963 (t70) cc_final: 0.8712 (p0) REVERT: E 206 GLN cc_start: 0.9013 (tp40) cc_final: 0.8605 (tp40) REVERT: E 211 THR cc_start: 0.8883 (t) cc_final: 0.8379 (m) REVERT: E 406 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8422 (mm-30) REVERT: F 54 TYR cc_start: 0.9035 (p90) cc_final: 0.8829 (p90) REVERT: F 162 GLU cc_start: 0.9014 (mp0) cc_final: 0.8743 (mt-10) REVERT: F 206 GLN cc_start: 0.8807 (mt0) cc_final: 0.8376 (pp30) REVERT: F 348 ILE cc_start: 0.9368 (mt) cc_final: 0.9161 (mt) REVERT: F 407 ASN cc_start: 0.8985 (p0) cc_final: 0.8712 (p0) REVERT: F 424 ASN cc_start: 0.9484 (t0) cc_final: 0.9217 (t0) REVERT: G 20 LEU cc_start: 0.8463 (mt) cc_final: 0.8184 (tt) REVERT: G 22 GLN cc_start: 0.8808 (mt0) cc_final: 0.8592 (mt0) REVERT: G 153 GLU cc_start: 0.8612 (tp30) cc_final: 0.8300 (tt0) REVERT: G 198 LYS cc_start: 0.9260 (tttt) cc_final: 0.9032 (tttp) REVERT: G 204 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8202 (tmm160) REVERT: H 15 LEU cc_start: 0.8378 (tt) cc_final: 0.7920 (tp) REVERT: H 59 VAL cc_start: 0.8796 (t) cc_final: 0.8481 (t) REVERT: H 61 ARG cc_start: 0.8429 (tpt90) cc_final: 0.8066 (tpt90) REVERT: I 24 LYS cc_start: 0.7512 (mtpp) cc_final: 0.6723 (pttt) REVERT: I 104 MET cc_start: 0.7498 (tpp) cc_final: 0.7129 (tpt) REVERT: J 12 VAL cc_start: 0.5976 (t) cc_final: 0.5696 (t) REVERT: K 115 LEU cc_start: 0.8364 (tm) cc_final: 0.7554 (pp) REVERT: L 11 GLU cc_start: 0.2608 (mt-10) cc_final: 0.1430 (mt-10) REVERT: L 31 LYS cc_start: 0.7021 (ptpt) cc_final: 0.6724 (ptpp) REVERT: L 119 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7965 (mmtt) outliers start: 6 outliers final: 3 residues processed: 1055 average time/residue: 0.2793 time to fit residues: 446.6395 Evaluate side-chains 666 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 663 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 0.5980 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 40.0000 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 50.0000 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 496 GLN B 290 ASN B 316 GLN B 425 ASN B 571 GLN C 145 HIS ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 249 HIS D 413 GLN D 428 GLN D 458 HIS ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 222 ASN E 249 HIS E 252 HIS E 338 GLN E 363 ASN E 428 GLN E 458 HIS G 68 GLN G 185 GLN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111523 restraints weight = 69451.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110327 restraints weight = 40533.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110997 restraints weight = 29557.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111299 restraints weight = 23906.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111817 restraints weight = 20961.645| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 40725 Z= 0.179 Angle : 0.669 10.959 55366 Z= 0.344 Chirality : 0.045 0.230 6419 Planarity : 0.005 0.058 7462 Dihedral : 5.751 116.284 6280 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.99 % Allowed : 11.38 % Favored : 85.63 % 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: -1.65 (0.10), residues: 5795 helix: 0.12 (0.08), residues: 3187 sheet: -2.24 (0.19), residues: 609 loop : -2.66 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 274 TYR 0.015 0.001 TYR D 288 PHE 0.019 0.001 PHE A 406 TRP 0.016 0.002 TRP B 438 HIS 0.005 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00406 (40725) covalent geometry : angle 0.66869 (55366) hydrogen bonds : bond 0.03950 ( 2649) hydrogen bonds : angle 4.55809 ( 7803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 710 time to evaluate : 1.227 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: A 26 ASP cc_start: 0.8419 (m-30) cc_final: 0.7564 (m-30) REVERT: A 55 THR cc_start: 0.9239 (p) cc_final: 0.8973 (p) REVERT: A 69 LEU cc_start: 0.8836 (mp) cc_final: 0.8402 (mt) REVERT: A 246 ASN cc_start: 0.8438 (p0) cc_final: 0.8154 (p0) REVERT: A 294 MET cc_start: 0.8505 (mtp) cc_final: 0.8271 (mtp) REVERT: A 408 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8013 (mtm-85) REVERT: A 452 ASP cc_start: 0.7790 (m-30) cc_final: 0.7401 (t0) REVERT: A 474 ASP cc_start: 0.7761 (t70) cc_final: 0.7528 (p0) REVERT: B 55 THR cc_start: 0.9090 (p) cc_final: 0.8798 (p) REVERT: B 276 LYS cc_start: 0.8472 (tptp) cc_final: 0.7724 (mtmt) REVERT: B 282 MET cc_start: 0.8536 (mmm) cc_final: 0.8224 (mmm) REVERT: B 436 ASP cc_start: 0.7640 (m-30) cc_final: 0.7341 (m-30) REVERT: B 500 TYR cc_start: 0.8181 (m-80) cc_final: 0.7776 (m-80) REVERT: C 236 VAL cc_start: 0.9205 (m) cc_final: 0.8942 (p) REVERT: C 363 GLU cc_start: 0.8589 (tp30) cc_final: 0.8023 (tp30) REVERT: C 392 SER cc_start: 0.8997 (p) cc_final: 0.8672 (p) REVERT: C 408 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8231 (ttt90) REVERT: C 461 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 491 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8085 (ttp80) REVERT: C 493 ASP cc_start: 0.8871 (t0) cc_final: 0.8540 (t0) REVERT: D 260 MET cc_start: 0.8875 (mmm) cc_final: 0.8511 (mmt) REVERT: D 318 ASP cc_start: 0.6406 (t70) cc_final: 0.6168 (t0) REVERT: D 380 ASP cc_start: 0.8382 (t0) cc_final: 0.7846 (t0) REVERT: D 381 GLN cc_start: 0.9229 (tp40) cc_final: 0.8887 (tp40) REVERT: E 206 GLN cc_start: 0.8260 (tp40) cc_final: 0.7865 (tp40) REVERT: E 392 ILE cc_start: 0.9008 (tp) cc_final: 0.8757 (tp) REVERT: F 424 ASN cc_start: 0.9289 (t0) cc_final: 0.8971 (t0) REVERT: G 180 GLN cc_start: 0.8294 (mt0) cc_final: 0.8053 (mt0) REVERT: G 185 GLN cc_start: 0.8802 (tt0) cc_final: 0.7970 (tt0) REVERT: G 198 LYS cc_start: 0.9000 (tttt) cc_final: 0.8764 (tttp) REVERT: H 15 LEU cc_start: 0.8218 (tt) cc_final: 0.7781 (tp) REVERT: H 47 VAL cc_start: 0.8633 (t) cc_final: 0.8336 (m) REVERT: I 74 ARG cc_start: 0.6737 (mmm160) cc_final: 0.6537 (mmm160) REVERT: I 80 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7097 (pp20) REVERT: I 104 MET cc_start: 0.7091 (tpp) cc_final: 0.6756 (tpt) REVERT: L 178 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8424 (tt) outliers start: 97 outliers final: 46 residues processed: 772 average time/residue: 0.2585 time to fit residues: 309.8226 Evaluate side-chains 640 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 593 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 178 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 185 optimal weight: 3.9990 chunk 516 optimal weight: 50.0000 chunk 165 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 446 optimal weight: 9.9990 chunk 454 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 425 ASN B 196 GLN B 425 ASN B 477 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN I 72 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111116 restraints weight = 69801.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109480 restraints weight = 43044.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109749 restraints weight = 33056.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110588 restraints weight = 25833.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110788 restraints weight = 20838.329| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40725 Z= 0.198 Angle : 0.653 11.125 55366 Z= 0.335 Chirality : 0.045 0.234 6419 Planarity : 0.005 0.052 7462 Dihedral : 5.356 104.751 6278 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.01 % Allowed : 13.91 % Favored : 82.08 % 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: -0.58 (0.11), residues: 5795 helix: 1.19 (0.09), residues: 3181 sheet: -2.20 (0.19), residues: 611 loop : -2.42 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 105 TYR 0.026 0.002 TYR E 29 PHE 0.020 0.002 PHE A 406 TRP 0.014 0.002 TRP A 330 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00458 (40725) covalent geometry : angle 0.65330 (55366) hydrogen bonds : bond 0.03823 ( 2649) hydrogen bonds : angle 4.32850 ( 7803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 629 time to evaluate : 1.462 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: A 26 ASP cc_start: 0.8375 (m-30) cc_final: 0.7643 (m-30) REVERT: A 55 THR cc_start: 0.9252 (p) cc_final: 0.8958 (t) REVERT: A 85 ASP cc_start: 0.7698 (p0) cc_final: 0.7459 (p0) REVERT: A 246 ASN cc_start: 0.8514 (p0) cc_final: 0.8258 (p0) REVERT: A 408 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8130 (mtm-85) REVERT: A 452 ASP cc_start: 0.7847 (m-30) cc_final: 0.7444 (t0) REVERT: A 460 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7960 (mtm-85) REVERT: A 474 ASP cc_start: 0.7874 (t70) cc_final: 0.7659 (p0) REVERT: A 567 MET cc_start: 0.8569 (mmm) cc_final: 0.8182 (mmp) REVERT: B 55 THR cc_start: 0.9090 (p) cc_final: 0.8806 (p) REVERT: B 154 ARG cc_start: 0.7122 (ptm-80) cc_final: 0.6918 (ptm-80) REVERT: B 276 LYS cc_start: 0.8597 (tptp) cc_final: 0.7792 (mtmt) REVERT: B 282 MET cc_start: 0.8505 (mmm) cc_final: 0.8248 (mmm) REVERT: B 500 TYR cc_start: 0.8187 (m-80) cc_final: 0.7766 (m-80) REVERT: C 341 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8608 (tt) REVERT: C 363 GLU cc_start: 0.8615 (tp30) cc_final: 0.8016 (tp30) REVERT: C 391 MET cc_start: 0.8577 (mmt) cc_final: 0.8203 (mmt) REVERT: C 461 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8540 (tm-30) REVERT: C 491 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8107 (ttp80) REVERT: C 493 ASP cc_start: 0.8806 (t0) cc_final: 0.8580 (t0) REVERT: C 536 ILE cc_start: 0.9001 (tp) cc_final: 0.8722 (mt) REVERT: D 260 MET cc_start: 0.8929 (mmm) cc_final: 0.8667 (mmm) REVERT: D 318 ASP cc_start: 0.6622 (t70) cc_final: 0.6252 (t0) REVERT: D 380 ASP cc_start: 0.8458 (t0) cc_final: 0.7993 (t0) REVERT: D 398 ILE cc_start: 0.9259 (pt) cc_final: 0.8937 (mt) REVERT: D 413 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8233 (tm-30) REVERT: E 4 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7520 (pp) REVERT: E 141 MET cc_start: 0.8467 (mmm) cc_final: 0.8242 (mmm) REVERT: E 206 GLN cc_start: 0.8239 (tp40) cc_final: 0.7857 (tp40) REVERT: E 210 ARG cc_start: 0.6906 (ttp80) cc_final: 0.6665 (ttp80) REVERT: E 402 ASP cc_start: 0.7923 (t0) cc_final: 0.7633 (t0) REVERT: F 206 GLN cc_start: 0.8238 (pp30) cc_final: 0.7806 (pp30) REVERT: G 105 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5814 (mtmm) REVERT: G 149 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (ttpt) REVERT: G 185 GLN cc_start: 0.8550 (tt0) cc_final: 0.7852 (tt0) REVERT: G 198 LYS cc_start: 0.8972 (tttt) cc_final: 0.8771 (tttp) REVERT: H 15 LEU cc_start: 0.8220 (tt) cc_final: 0.7733 (tp) REVERT: H 47 VAL cc_start: 0.8660 (t) cc_final: 0.8425 (p) REVERT: H 61 ARG cc_start: 0.7488 (tpt90) cc_final: 0.7249 (tpt170) REVERT: I 74 ARG cc_start: 0.6876 (mmm160) cc_final: 0.6631 (mmm160) REVERT: I 80 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7172 (pp20) REVERT: I 104 MET cc_start: 0.7032 (tpp) cc_final: 0.6654 (tpt) REVERT: J 145 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.5099 (mt-10) REVERT: K 74 ARG cc_start: 0.7647 (mmp-170) cc_final: 0.7315 (mmp80) REVERT: K 78 ARG cc_start: 0.7210 (tpm-80) cc_final: 0.6826 (ptp-170) REVERT: K 113 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7944 (tm) REVERT: K 117 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6439 (mt-10) outliers start: 130 outliers final: 72 residues processed: 714 average time/residue: 0.2587 time to fit residues: 288.5037 Evaluate side-chains 635 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 557 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 150 optimal weight: 5.9990 chunk 423 optimal weight: 0.9980 chunk 386 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 425 ASN B 425 ASN B 477 GLN C 290 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 GLN K 72 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110302 restraints weight = 69053.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110254 restraints weight = 41832.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110656 restraints weight = 27518.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111449 restraints weight = 23005.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111718 restraints weight = 19127.717| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40725 Z= 0.146 Angle : 0.613 13.404 55366 Z= 0.310 Chirality : 0.043 0.233 6419 Planarity : 0.004 0.048 7462 Dihedral : 5.057 93.793 6278 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.73 % Allowed : 15.61 % Favored : 80.66 % 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: -0.01 (0.11), residues: 5795 helix: 1.71 (0.09), residues: 3189 sheet: -2.03 (0.20), residues: 587 loop : -2.27 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 78 TYR 0.023 0.001 TYR E 29 PHE 0.016 0.001 PHE A 406 TRP 0.013 0.001 TRP C 117 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00332 (40725) covalent geometry : angle 0.61269 (55366) hydrogen bonds : bond 0.03550 ( 2649) hydrogen bonds : angle 4.16213 ( 7803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 630 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8308 (m-30) cc_final: 0.7636 (m-30) REVERT: A 246 ASN cc_start: 0.8453 (p0) cc_final: 0.8216 (p0) REVERT: A 408 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8250 (mtm-85) REVERT: A 452 ASP cc_start: 0.7773 (m-30) cc_final: 0.7376 (t0) REVERT: A 491 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7752 (mmt180) REVERT: B 19 MET cc_start: 0.8796 (mtp) cc_final: 0.8590 (mtm) REVERT: B 35 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9007 (mm) REVERT: B 55 THR cc_start: 0.9024 (p) cc_final: 0.8756 (p) REVERT: B 154 ARG cc_start: 0.7092 (ptm-80) cc_final: 0.6888 (ptm-80) REVERT: B 276 LYS cc_start: 0.8555 (tptp) cc_final: 0.7745 (mtmt) REVERT: B 282 MET cc_start: 0.8471 (mmm) cc_final: 0.8247 (mmm) REVERT: B 500 TYR cc_start: 0.8165 (m-80) cc_final: 0.7746 (m-80) REVERT: C 341 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8539 (tt) REVERT: C 363 GLU cc_start: 0.8555 (tp30) cc_final: 0.8008 (tp30) REVERT: C 391 MET cc_start: 0.8578 (mmt) cc_final: 0.8255 (mmt) REVERT: C 491 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8285 (ttp80) REVERT: C 493 ASP cc_start: 0.8740 (t0) cc_final: 0.8448 (t0) REVERT: D 260 MET cc_start: 0.8905 (mmm) cc_final: 0.8624 (mmm) REVERT: D 318 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6325 (t0) REVERT: D 380 ASP cc_start: 0.8408 (t0) cc_final: 0.8075 (t0) REVERT: D 398 ILE cc_start: 0.9248 (pt) cc_final: 0.8953 (mt) REVERT: D 413 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 7 GLU cc_start: 0.7789 (pt0) cc_final: 0.7384 (mt-10) REVERT: E 128 GLU cc_start: 0.8002 (pm20) cc_final: 0.7775 (pm20) REVERT: E 206 GLN cc_start: 0.8234 (tp40) cc_final: 0.7841 (tp40) REVERT: E 210 ARG cc_start: 0.6922 (ttp80) cc_final: 0.6675 (ttp80) REVERT: E 402 ASP cc_start: 0.7855 (t0) cc_final: 0.7508 (t0) REVERT: F 209 GLU cc_start: 0.6637 (pt0) cc_final: 0.6294 (pt0) REVERT: G 105 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.5973 (mtmm) REVERT: G 185 GLN cc_start: 0.8464 (tt0) cc_final: 0.8114 (tt0) REVERT: H 15 LEU cc_start: 0.8123 (tt) cc_final: 0.7598 (tp) REVERT: H 47 VAL cc_start: 0.8674 (t) cc_final: 0.8401 (p) REVERT: I 74 ARG cc_start: 0.6837 (mmm160) cc_final: 0.6635 (mmm160) REVERT: I 80 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7211 (pp20) REVERT: I 104 MET cc_start: 0.7081 (tpp) cc_final: 0.6784 (tpt) outliers start: 121 outliers final: 66 residues processed: 710 average time/residue: 0.2487 time to fit residues: 276.8119 Evaluate side-chains 633 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 563 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 406 optimal weight: 0.2980 chunk 519 optimal weight: 20.0000 chunk 370 optimal weight: 50.0000 chunk 169 optimal weight: 8.9990 chunk 38 optimal weight: 0.0170 chunk 334 optimal weight: 30.0000 chunk 459 optimal weight: 2.9990 chunk 477 optimal weight: 7.9990 chunk 346 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 overall best weight: 4.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 425 ASN B 425 ASN B 465 GLN B 477 GLN C 290 ASN C 477 GLN ** C 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110573 restraints weight = 69417.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109896 restraints weight = 41361.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110394 restraints weight = 28559.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110844 restraints weight = 23380.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112312 restraints weight = 20987.691| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 40725 Z= 0.158 Angle : 0.620 13.875 55366 Z= 0.312 Chirality : 0.044 0.241 6419 Planarity : 0.004 0.060 7462 Dihedral : 4.933 95.364 6278 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.13 % Allowed : 16.87 % Favored : 78.99 % 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: 0.32 (0.12), residues: 5795 helix: 1.97 (0.09), residues: 3189 sheet: -1.77 (0.21), residues: 542 loop : -2.15 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 47 TYR 0.024 0.001 TYR E 29 PHE 0.029 0.001 PHE G 39 TRP 0.014 0.001 TRP J 175 HIS 0.008 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00361 (40725) covalent geometry : angle 0.62008 (55366) hydrogen bonds : bond 0.03474 ( 2649) hydrogen bonds : angle 4.08485 ( 7803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 614 time to evaluate : 1.387 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: A 26 ASP cc_start: 0.8294 (m-30) cc_final: 0.7664 (m-30) REVERT: A 246 ASN cc_start: 0.8449 (p0) cc_final: 0.8175 (p0) REVERT: A 452 ASP cc_start: 0.7749 (m-30) cc_final: 0.7372 (t0) REVERT: A 491 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7710 (mmt180) REVERT: A 504 ASP cc_start: 0.8041 (t70) cc_final: 0.7595 (t70) REVERT: B 35 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9029 (mm) REVERT: B 55 THR cc_start: 0.9013 (p) cc_final: 0.8744 (p) REVERT: B 276 LYS cc_start: 0.8517 (tptp) cc_final: 0.7696 (mtmt) REVERT: B 282 MET cc_start: 0.8455 (mmm) cc_final: 0.8227 (mmm) REVERT: B 500 TYR cc_start: 0.8124 (m-80) cc_final: 0.7719 (m-80) REVERT: C 341 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8541 (tt) REVERT: C 363 GLU cc_start: 0.8555 (tp30) cc_final: 0.8053 (tp30) REVERT: C 391 MET cc_start: 0.8576 (mmt) cc_final: 0.8091 (mmt) REVERT: C 491 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8285 (ttp80) REVERT: C 493 ASP cc_start: 0.8745 (t0) cc_final: 0.8479 (t0) REVERT: C 536 ILE cc_start: 0.8953 (tp) cc_final: 0.8702 (mt) REVERT: D 260 MET cc_start: 0.8956 (mmm) cc_final: 0.8656 (mmm) REVERT: D 318 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6298 (t0) REVERT: D 380 ASP cc_start: 0.8375 (t0) cc_final: 0.8067 (t0) REVERT: D 398 ILE cc_start: 0.9249 (pt) cc_final: 0.8944 (mt) REVERT: D 413 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8118 (tm-30) REVERT: E 7 GLU cc_start: 0.7804 (pt0) cc_final: 0.7355 (mt-10) REVERT: E 128 GLU cc_start: 0.7952 (pm20) cc_final: 0.7618 (pm20) REVERT: E 206 GLN cc_start: 0.8239 (tp40) cc_final: 0.7872 (tp40) REVERT: E 392 ILE cc_start: 0.8776 (tp) cc_final: 0.8504 (tp) REVERT: E 402 ASP cc_start: 0.7807 (t0) cc_final: 0.7497 (t0) REVERT: G 105 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5971 (mtmm) REVERT: G 202 GLU cc_start: 0.7769 (pt0) cc_final: 0.7417 (tm-30) REVERT: H 15 LEU cc_start: 0.8169 (tt) cc_final: 0.7634 (tp) REVERT: H 47 VAL cc_start: 0.8709 (t) cc_final: 0.8437 (p) REVERT: H 79 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: I 80 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7205 (pp20) REVERT: I 104 MET cc_start: 0.7082 (tpp) cc_final: 0.6749 (tpt) REVERT: L 131 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6290 (pp) outliers start: 134 outliers final: 82 residues processed: 702 average time/residue: 0.2433 time to fit residues: 270.4539 Evaluate side-chains 660 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 572 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 331 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 512 optimal weight: 3.9990 chunk 282 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 chunk 326 optimal weight: 7.9990 chunk 468 optimal weight: 50.0000 chunk 317 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 425 ASN B 425 ASN C 290 ASN D 206 GLN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN K 72 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111342 restraints weight = 69301.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109875 restraints weight = 41913.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110990 restraints weight = 30330.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111744 restraints weight = 22622.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112254 restraints weight = 19465.665| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40725 Z= 0.140 Angle : 0.608 13.265 55366 Z= 0.306 Chirality : 0.043 0.222 6419 Planarity : 0.004 0.051 7462 Dihedral : 4.814 89.456 6278 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.07 % Allowed : 17.64 % Favored : 78.29 % 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: 0.49 (0.12), residues: 5795 helix: 2.11 (0.09), residues: 3191 sheet: -1.71 (0.21), residues: 560 loop : -2.07 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 47 TYR 0.018 0.001 TYR D 203 PHE 0.021 0.001 PHE H 100 TRP 0.015 0.001 TRP J 175 HIS 0.006 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00320 (40725) covalent geometry : angle 0.60815 (55366) hydrogen bonds : bond 0.03369 ( 2649) hydrogen bonds : angle 4.02087 ( 7803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 591 time to evaluate : 1.406 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: A 26 ASP cc_start: 0.8279 (m-30) cc_final: 0.7683 (m-30) REVERT: A 246 ASN cc_start: 0.8422 (p0) cc_final: 0.8180 (p0) REVERT: A 452 ASP cc_start: 0.7694 (m-30) cc_final: 0.7320 (t0) REVERT: A 460 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7787 (mtm-85) REVERT: A 491 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7820 (mmt180) REVERT: A 504 ASP cc_start: 0.8101 (t70) cc_final: 0.7644 (t70) REVERT: B 35 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9014 (mm) REVERT: B 55 THR cc_start: 0.9072 (p) cc_final: 0.8824 (p) REVERT: B 282 MET cc_start: 0.8437 (mmm) cc_final: 0.8190 (mmm) REVERT: B 500 TYR cc_start: 0.8104 (m-80) cc_final: 0.7688 (m-80) REVERT: C 341 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8575 (tt) REVERT: C 363 GLU cc_start: 0.8606 (tp30) cc_final: 0.8211 (tp30) REVERT: C 450 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8870 (tp) REVERT: C 464 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8507 (tp) REVERT: C 493 ASP cc_start: 0.8708 (t0) cc_final: 0.8456 (t0) REVERT: D 49 GLU cc_start: 0.7518 (tt0) cc_final: 0.7307 (tp30) REVERT: D 260 MET cc_start: 0.8971 (mmm) cc_final: 0.8667 (mmm) REVERT: D 318 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6289 (t0) REVERT: D 380 ASP cc_start: 0.8345 (t0) cc_final: 0.8070 (t0) REVERT: D 398 ILE cc_start: 0.9291 (pt) cc_final: 0.8999 (mt) REVERT: D 413 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7884 (tm-30) REVERT: E 7 GLU cc_start: 0.7776 (pt0) cc_final: 0.7331 (mt-10) REVERT: E 128 GLU cc_start: 0.7907 (pm20) cc_final: 0.7700 (pm20) REVERT: E 206 GLN cc_start: 0.8217 (tp40) cc_final: 0.7855 (tp40) REVERT: E 392 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8477 (tp) REVERT: E 402 ASP cc_start: 0.7853 (t0) cc_final: 0.7549 (t0) REVERT: F 411 TYR cc_start: 0.8713 (m-10) cc_final: 0.8186 (m-10) REVERT: G 105 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5933 (mtmm) REVERT: G 202 GLU cc_start: 0.7768 (pt0) cc_final: 0.7469 (tm-30) REVERT: H 15 LEU cc_start: 0.8168 (tt) cc_final: 0.7628 (tp) REVERT: H 47 VAL cc_start: 0.8704 (t) cc_final: 0.8436 (p) REVERT: I 49 LYS cc_start: 0.7131 (mttm) cc_final: 0.6894 (mmmt) REVERT: I 80 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7155 (pp20) REVERT: I 104 MET cc_start: 0.7043 (tpp) cc_final: 0.6733 (tpt) outliers start: 132 outliers final: 90 residues processed: 675 average time/residue: 0.2383 time to fit residues: 256.4361 Evaluate side-chains 661 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 564 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 559 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 505 optimal weight: 30.0000 chunk 438 optimal weight: 30.0000 chunk 372 optimal weight: 40.0000 chunk 47 optimal weight: 20.0000 chunk 437 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 361 optimal weight: 0.0670 overall best weight: 6.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 425 ASN B 290 ASN B 316 GLN B 425 ASN C 290 ASN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN E 222 ASN F 375 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110086 restraints weight = 69851.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107829 restraints weight = 44894.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108634 restraints weight = 35600.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109521 restraints weight = 25387.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110382 restraints weight = 20119.885| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 40725 Z= 0.204 Angle : 0.644 12.648 55366 Z= 0.325 Chirality : 0.045 0.212 6419 Planarity : 0.004 0.088 7462 Dihedral : 4.842 82.777 6278 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.32 % Allowed : 17.74 % Favored : 77.95 % 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: 0.55 (0.12), residues: 5795 helix: 2.15 (0.09), residues: 3204 sheet: -1.70 (0.21), residues: 548 loop : -2.06 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 36 TYR 0.019 0.001 TYR D 203 PHE 0.030 0.001 PHE G 39 TRP 0.014 0.001 TRP A 330 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00477 (40725) covalent geometry : angle 0.64373 (55366) hydrogen bonds : bond 0.03517 ( 2649) hydrogen bonds : angle 4.05037 ( 7803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 567 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8281 (m-30) cc_final: 0.7717 (m-30) REVERT: A 246 ASN cc_start: 0.8463 (p0) cc_final: 0.8222 (p0) REVERT: A 452 ASP cc_start: 0.7727 (m-30) cc_final: 0.7392 (t0) REVERT: A 460 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7618 (mtm-85) REVERT: A 491 ARG cc_start: 0.8150 (mtm110) cc_final: 0.7839 (mmt180) REVERT: B 35 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9072 (mm) REVERT: B 55 THR cc_start: 0.9041 (p) cc_final: 0.8781 (p) REVERT: B 282 MET cc_start: 0.8348 (mmm) cc_final: 0.8058 (mmm) REVERT: B 500 TYR cc_start: 0.8151 (m-80) cc_final: 0.7710 (m-80) REVERT: C 341 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8583 (tt) REVERT: C 363 GLU cc_start: 0.8637 (tp30) cc_final: 0.8202 (tp30) REVERT: C 450 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8930 (tp) REVERT: C 464 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8466 (tp) REVERT: C 481 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7872 (tpp-160) REVERT: C 493 ASP cc_start: 0.8774 (t0) cc_final: 0.8507 (t0) REVERT: D 260 MET cc_start: 0.8981 (mmm) cc_final: 0.8683 (mmm) REVERT: D 380 ASP cc_start: 0.8431 (t0) cc_final: 0.8146 (t0) REVERT: D 398 ILE cc_start: 0.9308 (pt) cc_final: 0.9002 (mt) REVERT: D 432 ILE cc_start: 0.9064 (tp) cc_final: 0.8808 (tp) REVERT: E 7 GLU cc_start: 0.7814 (pt0) cc_final: 0.7402 (mt-10) REVERT: E 206 GLN cc_start: 0.8190 (tp40) cc_final: 0.7795 (tp40) REVERT: E 392 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8540 (tp) REVERT: F 77 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7441 (mt-10) REVERT: G 105 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.5954 (mtmm) REVERT: G 202 GLU cc_start: 0.7826 (pt0) cc_final: 0.7479 (tm-30) REVERT: H 15 LEU cc_start: 0.8189 (tt) cc_final: 0.7619 (tp) REVERT: H 47 VAL cc_start: 0.8716 (t) cc_final: 0.8439 (p) REVERT: H 79 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: I 24 LYS cc_start: 0.6980 (mtpp) cc_final: 0.6314 (pttt) REVERT: I 80 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7193 (pp20) REVERT: I 104 MET cc_start: 0.6914 (tpp) cc_final: 0.6622 (tpt) REVERT: K 74 ARG cc_start: 0.7899 (mmp-170) cc_final: 0.7377 (mmp80) REVERT: L 131 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6201 (pp) outliers start: 140 outliers final: 103 residues processed: 662 average time/residue: 0.2425 time to fit residues: 254.5872 Evaluate side-chains 654 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 543 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 189 optimal weight: 9.9990 chunk 565 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 330 optimal weight: 30.0000 chunk 215 optimal weight: 0.2980 chunk 557 optimal weight: 50.0000 chunk 196 optimal weight: 0.9990 chunk 372 optimal weight: 20.0000 chunk 308 optimal weight: 6.9990 chunk 456 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 290 ASN B 425 ASN B 477 GLN C 290 ASN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110890 restraints weight = 69300.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109560 restraints weight = 42166.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110678 restraints weight = 29413.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111104 restraints weight = 22675.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111563 restraints weight = 20292.684| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40725 Z= 0.141 Angle : 0.615 12.608 55366 Z= 0.309 Chirality : 0.043 0.201 6419 Planarity : 0.004 0.071 7462 Dihedral : 4.727 75.591 6278 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.82 % Allowed : 18.32 % Favored : 77.85 % 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: 0.69 (0.12), residues: 5795 helix: 2.26 (0.09), residues: 3196 sheet: -1.69 (0.21), residues: 573 loop : -1.94 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 58 TYR 0.021 0.001 TYR D 203 PHE 0.029 0.001 PHE G 39 TRP 0.019 0.001 TRP C 117 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00323 (40725) covalent geometry : angle 0.61544 (55366) hydrogen bonds : bond 0.03339 ( 2649) hydrogen bonds : angle 3.96433 ( 7803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 573 time to evaluate : 1.382 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: A 26 ASP cc_start: 0.8213 (m-30) cc_final: 0.7628 (m-30) REVERT: A 212 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9212 (mp) REVERT: A 246 ASN cc_start: 0.8426 (p0) cc_final: 0.8202 (p0) REVERT: A 452 ASP cc_start: 0.7706 (m-30) cc_final: 0.7323 (t0) REVERT: A 460 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7754 (mtm-85) REVERT: A 491 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7719 (mmt180) REVERT: A 498 ASN cc_start: 0.8133 (p0) cc_final: 0.7914 (p0) REVERT: A 504 ASP cc_start: 0.8045 (t70) cc_final: 0.7680 (t70) REVERT: B 35 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9031 (mm) REVERT: B 55 THR cc_start: 0.9094 (p) cc_final: 0.8849 (p) REVERT: B 500 TYR cc_start: 0.8140 (m-80) cc_final: 0.7697 (m-80) REVERT: C 220 MET cc_start: 0.8277 (tpt) cc_final: 0.8037 (tpt) REVERT: C 290 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8259 (m-40) REVERT: C 341 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8593 (tt) REVERT: C 363 GLU cc_start: 0.8597 (tp30) cc_final: 0.8230 (tp30) REVERT: C 450 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8911 (tp) REVERT: C 464 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8512 (tp) REVERT: C 493 ASP cc_start: 0.8725 (t0) cc_final: 0.8458 (t0) REVERT: C 540 LEU cc_start: 0.8674 (mt) cc_final: 0.8461 (mt) REVERT: D 49 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: D 260 MET cc_start: 0.8968 (mmm) cc_final: 0.8662 (mmm) REVERT: D 380 ASP cc_start: 0.8414 (t0) cc_final: 0.8123 (t0) REVERT: D 398 ILE cc_start: 0.9295 (pt) cc_final: 0.8995 (mt) REVERT: D 432 ILE cc_start: 0.9005 (tp) cc_final: 0.8796 (tp) REVERT: E 7 GLU cc_start: 0.7791 (pt0) cc_final: 0.7407 (mt-10) REVERT: E 206 GLN cc_start: 0.8117 (tp40) cc_final: 0.7723 (tp40) REVERT: E 392 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8504 (tp) REVERT: F 77 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7350 (mt-10) REVERT: G 105 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5959 (mtmm) REVERT: G 202 GLU cc_start: 0.7782 (pt0) cc_final: 0.7351 (tm-30) REVERT: H 15 LEU cc_start: 0.8181 (tt) cc_final: 0.7630 (tp) REVERT: H 47 VAL cc_start: 0.8712 (t) cc_final: 0.8481 (p) REVERT: I 80 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7206 (pp20) REVERT: I 104 MET cc_start: 0.6915 (tpp) cc_final: 0.6604 (tpt) REVERT: K 74 ARG cc_start: 0.7853 (mmp-170) cc_final: 0.7357 (mmp80) REVERT: L 131 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6271 (pp) outliers start: 124 outliers final: 92 residues processed: 655 average time/residue: 0.2410 time to fit residues: 252.2515 Evaluate side-chains 655 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 553 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 351 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 chunk 562 optimal weight: 7.9990 chunk 468 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 537 optimal weight: 50.0000 chunk 39 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 553 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 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 425 ASN B 290 ASN B 425 ASN C 290 ASN D 375 HIS ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN L 10 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.138421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108993 restraints weight = 69874.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106856 restraints weight = 45891.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107252 restraints weight = 33694.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107721 restraints weight = 28380.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108090 restraints weight = 22545.908| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 40725 Z= 0.249 Angle : 0.688 12.429 55366 Z= 0.348 Chirality : 0.046 0.195 6419 Planarity : 0.005 0.066 7462 Dihedral : 4.874 65.787 6278 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.82 % Allowed : 19.00 % Favored : 77.17 % 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: 0.66 (0.12), residues: 5795 helix: 2.26 (0.09), residues: 3196 sheet: -1.74 (0.21), residues: 563 loop : -2.00 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 36 TYR 0.022 0.002 TYR D 203 PHE 0.031 0.002 PHE G 39 TRP 0.019 0.002 TRP J 175 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00583 (40725) covalent geometry : angle 0.68804 (55366) hydrogen bonds : bond 0.03628 ( 2649) hydrogen bonds : angle 4.07356 ( 7803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 555 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8316 (m-30) cc_final: 0.7757 (m-30) REVERT: A 246 ASN cc_start: 0.8500 (p0) cc_final: 0.8246 (p0) REVERT: A 452 ASP cc_start: 0.7700 (m-30) cc_final: 0.7439 (t0) REVERT: A 460 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7489 (mtm-85) REVERT: A 491 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7772 (mmt180) REVERT: B 35 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9054 (mm) REVERT: B 55 THR cc_start: 0.9088 (p) cc_final: 0.8834 (p) REVERT: B 261 GLU cc_start: 0.7771 (tt0) cc_final: 0.7514 (tm-30) REVERT: B 330 TRP cc_start: 0.9200 (t60) cc_final: 0.8993 (t60) REVERT: B 500 TYR cc_start: 0.8180 (m-80) cc_final: 0.7743 (m-80) REVERT: C 290 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8271 (m-40) REVERT: C 341 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8611 (tt) REVERT: C 363 GLU cc_start: 0.8720 (tp30) cc_final: 0.8325 (tp30) REVERT: C 392 SER cc_start: 0.9020 (p) cc_final: 0.8705 (p) REVERT: C 450 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8944 (tp) REVERT: C 481 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7950 (tpp-160) REVERT: C 493 ASP cc_start: 0.8775 (t0) cc_final: 0.8567 (t0) REVERT: D 260 MET cc_start: 0.8967 (mmm) cc_final: 0.8710 (mmm) REVERT: D 380 ASP cc_start: 0.8438 (t0) cc_final: 0.8156 (t0) REVERT: D 398 ILE cc_start: 0.9297 (pt) cc_final: 0.9021 (mt) REVERT: D 432 ILE cc_start: 0.9042 (tp) cc_final: 0.8792 (tp) REVERT: E 7 GLU cc_start: 0.7852 (pt0) cc_final: 0.7485 (mt-10) REVERT: E 206 GLN cc_start: 0.8182 (tp40) cc_final: 0.7762 (tp40) REVERT: E 392 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8550 (tp) REVERT: F 77 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7466 (mt-10) REVERT: G 105 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6113 (mtmm) REVERT: G 202 GLU cc_start: 0.7853 (pt0) cc_final: 0.7422 (tm-30) REVERT: H 15 LEU cc_start: 0.8147 (tt) cc_final: 0.7586 (tp) REVERT: H 47 VAL cc_start: 0.8720 (t) cc_final: 0.8495 (p) REVERT: I 74 ARG cc_start: 0.6578 (mmm160) cc_final: 0.6364 (mmm160) REVERT: I 80 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7224 (pp20) REVERT: I 104 MET cc_start: 0.6893 (tpp) cc_final: 0.6587 (tpt) REVERT: J 74 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: K 74 ARG cc_start: 0.7970 (mmp-170) cc_final: 0.7443 (mmp80) REVERT: L 84 ARG cc_start: 0.6689 (ttp-110) cc_final: 0.6463 (ttp80) REVERT: L 131 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6319 (pp) outliers start: 124 outliers final: 102 residues processed: 634 average time/residue: 0.2440 time to fit residues: 246.2709 Evaluate side-chains 651 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 541 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 560 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 452 optimal weight: 30.0000 chunk 442 optimal weight: 40.0000 chunk 312 optimal weight: 9.9990 chunk 386 optimal weight: 7.9990 chunk 368 optimal weight: 6.9990 chunk 443 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 425 ASN B 290 ASN B 425 ASN B 477 GLN C 290 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109099 restraints weight = 69440.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106926 restraints weight = 41881.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108626 restraints weight = 30204.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109057 restraints weight = 19886.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109065 restraints weight = 17294.838| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 40725 Z= 0.217 Angle : 0.678 12.178 55366 Z= 0.342 Chirality : 0.045 0.200 6419 Planarity : 0.005 0.064 7462 Dihedral : 4.849 55.113 6278 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.70 % Allowed : 19.25 % Favored : 77.05 % 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: 0.72 (0.12), residues: 5795 helix: 2.30 (0.09), residues: 3189 sheet: -1.67 (0.22), residues: 545 loop : -1.95 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 408 TYR 0.023 0.002 TYR D 203 PHE 0.030 0.001 PHE G 39 TRP 0.018 0.001 TRP J 175 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00509 (40725) covalent geometry : angle 0.67839 (55366) hydrogen bonds : bond 0.03573 ( 2649) hydrogen bonds : angle 4.05999 ( 7803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11590 Ramachandran restraints generated. 5795 Oldfield, 0 Emsley, 5795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 548 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8299 (m-30) cc_final: 0.7734 (m-30) REVERT: A 246 ASN cc_start: 0.8463 (p0) cc_final: 0.8237 (p0) REVERT: A 452 ASP cc_start: 0.7692 (m-30) cc_final: 0.7322 (t0) REVERT: A 460 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7606 (mtm-85) REVERT: A 491 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7802 (mmt180) REVERT: B 35 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9017 (mm) REVERT: B 55 THR cc_start: 0.9099 (p) cc_final: 0.8831 (p) REVERT: B 330 TRP cc_start: 0.9164 (t60) cc_final: 0.8917 (t60) REVERT: B 500 TYR cc_start: 0.8209 (m-80) cc_final: 0.7774 (m-80) REVERT: C 290 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8337 (m-40) REVERT: C 341 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8579 (tt) REVERT: C 363 GLU cc_start: 0.8627 (tp30) cc_final: 0.8194 (tp30) REVERT: C 392 SER cc_start: 0.9010 (p) cc_final: 0.8694 (p) REVERT: C 450 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8919 (tp) REVERT: C 481 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7898 (tpp-160) REVERT: C 493 ASP cc_start: 0.8791 (t0) cc_final: 0.8586 (t0) REVERT: D 380 ASP cc_start: 0.8433 (t0) cc_final: 0.8157 (t0) REVERT: D 398 ILE cc_start: 0.9306 (pt) cc_final: 0.9028 (mt) REVERT: D 432 ILE cc_start: 0.9015 (tp) cc_final: 0.8769 (tp) REVERT: E 7 GLU cc_start: 0.7835 (pt0) cc_final: 0.7436 (mt-10) REVERT: E 206 GLN cc_start: 0.8195 (tp40) cc_final: 0.7745 (tp40) REVERT: E 392 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8553 (tp) REVERT: F 77 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7457 (mt-10) REVERT: G 105 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6033 (mmmm) REVERT: G 202 GLU cc_start: 0.7838 (pt0) cc_final: 0.7446 (tm-30) REVERT: H 1 MET cc_start: 0.6796 (tpp) cc_final: 0.6535 (tpp) REVERT: H 15 LEU cc_start: 0.8150 (tt) cc_final: 0.7604 (tp) REVERT: H 47 VAL cc_start: 0.8753 (t) cc_final: 0.8543 (p) REVERT: H 79 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: I 74 ARG cc_start: 0.6615 (mmm160) cc_final: 0.6373 (mmm160) REVERT: I 80 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7201 (pp20) REVERT: I 104 MET cc_start: 0.6911 (tpp) cc_final: 0.6305 (tpt) REVERT: L 100 TRP cc_start: 0.7141 (t-100) cc_final: 0.6338 (t-100) REVERT: L 131 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6272 (pp) outliers start: 120 outliers final: 101 residues processed: 625 average time/residue: 0.2379 time to fit residues: 236.2470 Evaluate side-chains 649 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 540 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 179 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 346 optimal weight: 40.0000 chunk 315 optimal weight: 20.0000 chunk 391 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 395 optimal weight: 1.9990 chunk 301 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 290 ASN B 425 ASN B 477 GLN C 290 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108513 restraints weight = 69696.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107264 restraints weight = 44141.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108232 restraints weight = 30293.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108824 restraints weight = 23908.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109352 restraints weight = 19884.486| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 40725 Z= 0.197 Angle : 0.666 12.027 55366 Z= 0.336 Chirality : 0.045 0.193 6419 Planarity : 0.004 0.061 7462 Dihedral : 4.780 50.271 6278 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.89 % Allowed : 19.25 % Favored : 76.87 % 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: 0.79 (0.12), residues: 5795 helix: 2.34 (0.09), residues: 3184 sheet: -1.70 (0.21), residues: 553 loop : -1.86 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 130 TYR 0.024 0.001 TYR D 203 PHE 0.029 0.001 PHE G 39 TRP 0.016 0.001 TRP J 175 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00461 (40725) covalent geometry : angle 0.66614 (55366) hydrogen bonds : bond 0.03527 ( 2649) hydrogen bonds : angle 4.04187 ( 7803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6958.72 seconds wall clock time: 120 minutes 20.97 seconds (7220.97 seconds total)