Starting phenix.real_space_refine on Tue Aug 26 09:14:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0a_29651/08_2025/8g0a_29651.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0a_29651/08_2025/8g0a_29651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g0a_29651/08_2025/8g0a_29651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0a_29651/08_2025/8g0a_29651.map" model { file = "/net/cci-nas-00/data/ceres_data/8g0a_29651/08_2025/8g0a_29651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0a_29651/08_2025/8g0a_29651.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.096 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 13 5.49 5 Mg 4 5.21 5 S 103 5.16 5 C 22700 2.51 5 N 6238 2.21 5 O 6572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35630 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3827 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 492} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 3733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3733 Classifications: {'peptide': 507} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 9, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3797 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 11, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3505 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3527 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2094 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 9, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 838 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 59 Chain: "b" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 941 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 84 Chain: "d" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2875 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 11, 'TRANS': 421} Chain breaks: 1 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 9, 'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 270 Chain: "2" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "3" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "4" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "5" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "6" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "8" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1808 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "1" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'SQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.47, per 1000 atoms: 0.18 Number of scatterers: 35630 At special positions: 0 Unit cell: (136.99, 123.6, 242.05, 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 13 15.00 Mg 4 11.99 O 6572 8.00 N 6238 7.00 C 22700 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8748 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 20 sheets defined 61.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 22 removed outlier: 3.559A pdb=" N GLU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.522A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.699A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.501A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.673A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.932A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 5.055A pdb=" N SER A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.160A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.804A pdb=" N GLU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.716A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.555A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.669A pdb=" N GLU B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.659A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.560A pdb=" N GLN B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 408 removed outlier: 5.136A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.781A pdb=" N GLU B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 removed outlier: 3.780A pdb=" N VAL B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.424A pdb=" N PHE B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.769A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.760A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 removed outlier: 3.716A pdb=" N GLU C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 263 Proline residue: C 250 - end of helix removed outlier: 3.673A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 289 Processing helix chain 'C' and resid 293 through 297 removed outlier: 3.756A pdb=" N ALA C 296 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 299 No H-bonds generated for 'chain 'C' and resid 298 through 299' Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.742A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 414 through 432 Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.305A pdb=" N PHE C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.612A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 147 Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.679A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 270 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 317 through 324 Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 362 through 390 removed outlier: 4.076A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 395 through 412 removed outlier: 3.523A pdb=" N ARG D 407 " --> pdb=" O ASN D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 451 through 455 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.763A pdb=" N ALA E 46 " --> pdb=" O GLY E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 178 through 181 Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 5.471A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 271 removed outlier: 3.778A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 291 Processing helix chain 'E' and resid 311 through 314 Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 362 through 389 removed outlier: 4.768A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 removed outlier: 3.669A pdb=" N GLU E 393 " --> pdb=" O GLY E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 removed outlier: 3.713A pdb=" N ARG E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 451 through 455 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.184A pdb=" N VAL F 29 " --> pdb=" O ARG F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 126 through 130 Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 223 through 244 removed outlier: 4.427A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 268 removed outlier: 4.100A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 295 removed outlier: 4.196A pdb=" N ARG F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR F 295 " --> pdb=" O GLN F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.646A pdb=" N LYS F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 382 removed outlier: 3.702A pdb=" N TYR F 366 " --> pdb=" O GLY F 362 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 389 Processing helix chain 'F' and resid 390 through 394 Processing helix chain 'F' and resid 395 through 413 removed outlier: 3.535A pdb=" N SER F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 419 through 424 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 460 through 471 Processing helix chain 'G' and resid 5 through 60 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 163 Processing helix chain 'G' and resid 227 through 301 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 91 through 99 Processing helix chain 'H' and resid 103 through 118 Processing helix chain 'b' and resid 29 through 49 Processing helix chain 'b' and resid 49 through 160 removed outlier: 3.673A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 138 removed outlier: 3.701A pdb=" N GLU d 75 " --> pdb=" O LYS d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 156 Processing helix chain 'd' and resid 173 through 192 Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 225 Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.550A pdb=" N LEU d 250 " --> pdb=" O SER d 246 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP d 251 " --> pdb=" O ALA d 247 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU d 252 " --> pdb=" O THR d 248 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 287 removed outlier: 3.964A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU d 279 " --> pdb=" O ALA d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 Processing helix chain 'd' and resid 306 through 313 Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 3.668A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 385 through 402 Processing helix chain 'd' and resid 412 through 416 removed outlier: 3.612A pdb=" N LEU d 415 " --> pdb=" O ASP d 412 " (cutoff:3.500A) Processing helix chain 'd' and resid 431 through 443 Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 48 through 81 removed outlier: 4.268A pdb=" N ARG 2 52 " --> pdb=" O GLU 2 48 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE 2 54 " --> pdb=" O GLN 2 50 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 3.763A pdb=" N ALA 2 67 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR 2 68 " --> pdb=" O VAL 2 64 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 81 removed outlier: 4.394A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 80 removed outlier: 4.409A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix Processing helix chain '5' and resid 6 through 46 Processing helix chain '5' and resid 49 through 81 removed outlier: 3.669A pdb=" N PHE 5 54 " --> pdb=" O GLN 5 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR 5 55 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 46 Processing helix chain '6' and resid 49 through 80 removed outlier: 3.847A pdb=" N THR 6 55 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) Proline residue: 6 56 - end of helix Processing helix chain '7' and resid 6 through 46 Processing helix chain '7' and resid 49 through 80 removed outlier: 4.500A pdb=" N THR 7 55 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 6 through 46 Processing helix chain '8' and resid 48 through 80 removed outlier: 4.102A pdb=" N ARG 8 52 " --> pdb=" O GLU 8 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE 8 54 " --> pdb=" O GLN 8 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 49 through 80 removed outlier: 4.024A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix Processing helix chain 'a' and resid 28 through 52 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.576A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR a 95 " --> pdb=" O PRO a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.745A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 204 removed outlier: 3.634A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU a 177 " --> pdb=" O ILE a 173 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.828A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.561A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain '1' and resid 6 through 46 Processing helix chain '1' and resid 48 through 53 removed outlier: 4.205A pdb=" N ARG 1 52 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 80 removed outlier: 3.775A pdb=" N ALA 1 67 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR 1 68 " --> pdb=" O VAL 1 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE 1 80 " --> pdb=" O ALA 1 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 38 removed outlier: 5.565A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 46 current: chain 'A' and resid 63 through 69 removed outlier: 5.729A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 74 through 78 current: chain 'C' and resid 41 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 41 through 45 current: chain 'C' and resid 63 through 69 removed outlier: 4.175A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU C 69 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 79 current: chain 'D' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 23 current: chain 'D' and resid 47 through 58 removed outlier: 6.591A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 61 through 66 current: chain 'F' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 23 current: chain 'F' and resid 47 through 58 removed outlier: 6.566A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 61 through 66 current: chain 'd' and resid 405 through 409 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 405 through 409 current: chain 'd' and resid 426 through 429 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 110 through 111 current: chain 'A' and resid 232 through 237 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 232 through 237 current: chain 'A' and resid 323 through 331 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 323 through 331 current: chain 'A' and resid 374 through 375 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 69 removed outlier: 4.044A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU E 78 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU E 39 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA E 35 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.601A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG B 203 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL B 270 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 205 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 272 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 207 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 267 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU B 327 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE B 269 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 329 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 271 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLU B 331 " --> pdb=" O PHE B 271 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.522A pdb=" N PHE C 271 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 330 " --> pdb=" O ILE C 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 534 through 540 removed outlier: 11.335A pdb=" N GLU C 534 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU C 536 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G 191 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU G 116 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER G 137 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL G 118 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.091A pdb=" N GLU D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 98 through 99 current: chain 'D' and resid 213 through 219 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 213 through 219 current: chain 'D' and resid 300 through 307 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 300 through 307 current: chain 'D' and resid 352 through 353 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.918A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 98 through 100 removed outlier: 6.856A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY E 189 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR E 309 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL E 308 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU E 158 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS E 155 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR E 331 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA E 157 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.902A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.728A pdb=" N SER F 185 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL F 216 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE F 187 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY F 218 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY F 189 " --> pdb=" O GLY F 218 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS F 155 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR F 331 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA F 157 " --> pdb=" O THR F 331 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 135 through 137 removed outlier: 4.705A pdb=" N GLU F 135 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 223 through 225 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 223 through 225 current: chain 'H' and resid 14 through 16 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 14 through 16 current: chain 'H' and resid 69 through 72 Processing sheet with id=AB9, first strand: chain 'H' and resid 30 through 34 removed outlier: 3.868A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AC2, first strand: chain 'a' and resid 112 through 114 2293 hydrogen bonds defined for protein. 6627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5950 1.28 - 1.41: 8401 1.41 - 1.54: 21620 1.54 - 1.68: 73 1.68 - 1.81: 186 Bond restraints: 36230 Sorted by residual: bond pdb=" CA ARG F 272 " pdb=" C ARG F 272 " ideal model delta sigma weight residual 1.523 1.428 0.095 1.18e-02 7.18e+03 6.53e+01 bond pdb=" CA ALA E 454 " pdb=" C ALA E 454 " ideal model delta sigma weight residual 1.523 1.409 0.113 1.41e-02 5.03e+03 6.46e+01 bond pdb=" C PHE a 221 " pdb=" O PHE a 221 " ideal model delta sigma weight residual 1.237 1.144 0.092 1.17e-02 7.31e+03 6.24e+01 bond pdb=" C ASN 6 6 " pdb=" O ASN 6 6 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.17e-02 7.31e+03 5.98e+01 bond pdb=" CA TYR F 379 " pdb=" C TYR F 379 " ideal model delta sigma weight residual 1.523 1.419 0.104 1.41e-02 5.03e+03 5.44e+01 ... (remaining 36225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 48222 2.38 - 4.76: 822 4.76 - 7.13: 147 7.13 - 9.51: 19 9.51 - 11.89: 3 Bond angle restraints: 49213 Sorted by residual: angle pdb=" N GLY H 118 " pdb=" CA GLY H 118 " pdb=" C GLY H 118 " ideal model delta sigma weight residual 115.21 103.32 11.89 1.30e+00 5.92e-01 8.36e+01 angle pdb=" N ASP B 10 " pdb=" CA ASP B 10 " pdb=" C ASP B 10 " ideal model delta sigma weight residual 111.82 101.37 10.45 1.16e+00 7.43e-01 8.12e+01 angle pdb=" N LYS D 467 " pdb=" CA LYS D 467 " pdb=" C LYS D 467 " ideal model delta sigma weight residual 113.38 103.89 9.49 1.23e+00 6.61e-01 5.95e+01 angle pdb=" N ARG E 293 " pdb=" CA ARG E 293 " pdb=" C ARG E 293 " ideal model delta sigma weight residual 113.97 104.11 9.86 1.28e+00 6.10e-01 5.94e+01 angle pdb=" N ILE d 98 " pdb=" CA ILE d 98 " pdb=" C ILE d 98 " ideal model delta sigma weight residual 110.72 118.09 -7.37 1.01e+00 9.80e-01 5.33e+01 ... (remaining 49208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19848 17.97 - 35.95: 1345 35.95 - 53.92: 335 53.92 - 71.90: 92 71.90 - 89.87: 25 Dihedral angle restraints: 21645 sinusoidal: 7990 harmonic: 13655 Sorted by residual: dihedral pdb=" CA PHE D 343 " pdb=" C PHE D 343 " pdb=" N PRO D 344 " pdb=" CA PRO D 344 " ideal model delta harmonic sigma weight residual 0.00 25.17 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE F 343 " pdb=" C PHE F 343 " pdb=" N PRO F 344 " pdb=" CA PRO F 344 " ideal model delta harmonic sigma weight residual 0.00 22.76 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" C ALA C 367 " pdb=" N ALA C 367 " pdb=" CA ALA C 367 " pdb=" CB ALA C 367 " ideal model delta harmonic sigma weight residual -122.60 -133.54 10.94 0 2.50e+00 1.60e-01 1.92e+01 ... (remaining 21642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5364 0.085 - 0.170: 416 0.170 - 0.255: 32 0.255 - 0.341: 13 0.341 - 0.426: 2 Chirality restraints: 5827 Sorted by residual: chirality pdb=" CA ALA C 367 " pdb=" N ALA C 367 " pdb=" C ALA C 367 " pdb=" CB ALA C 367 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA PRO D 344 " pdb=" N PRO D 344 " pdb=" C PRO D 344 " pdb=" CB PRO D 344 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA ALA F 345 " pdb=" N ALA F 345 " pdb=" C ALA F 345 " pdb=" CB ALA F 345 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 5824 not shown) Planarity restraints: 6370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 271 " -0.072 2.00e-02 2.50e+03 4.53e-02 3.59e+01 pdb=" CG PHE C 271 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 271 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE C 271 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE C 271 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 271 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 271 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 115 " 0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C ARG H 115 " -0.080 2.00e-02 2.50e+03 pdb=" O ARG H 115 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA H 116 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 271 " -0.053 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 271 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 271 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 271 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A 271 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 271 " -0.032 2.00e-02 2.50e+03 ... (remaining 6367 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 89 2.43 - 3.05: 25383 3.05 - 3.67: 55467 3.67 - 4.28: 85684 4.28 - 4.90: 144355 Nonbonded interactions: 310978 Sorted by model distance: nonbonded pdb=" O2G ATP E 600 " pdb="MG MG E 601 " model vdw 1.816 2.170 nonbonded pdb=" OG1 THR B 179 " pdb="MG MG B 601 " model vdw 1.857 2.170 nonbonded pdb=" OG1 THR A 179 " pdb="MG MG A 601 " model vdw 1.874 2.170 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.879 2.170 nonbonded pdb=" OD2 ASP A 272 " pdb="MG MG A 601 " model vdw 1.945 2.170 ... (remaining 310973 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 '1' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '2' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '3' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 85)) selection = (chain '4' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '6' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '7' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '8' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '9' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) } ncs_group { reference = (chain 'A' and ((resid 9 through 12 and (name N or name CA or name C or name O o \ r name CB )) or (resid 13 through 22 and (name N or name CA or name C or name O \ or name CB )) or (resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 35 or (resid 36 through 37 and (name N or name CA or nam \ e C or name O or name CB )) or resid 38 or (resid 39 and (name N or name CA or n \ ame C or name O or name CB )) or resid 40 through 82 or (resid 83 and (name N or \ name CA or name C or name O or name CB )) or resid 84 through 294 or (resid 295 \ through 296 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 97 through 317 or (resid 318 and (name N or name CA or name C or name O or name \ CB )) or resid 319 through 357 or (resid 358 and (name N or name CA or name C or \ name O or name CB )) or resid 359 through 394 or (resid 395 through 396 and (na \ me N or name CA or name C or name O or name CB )) or resid 397 through 410 or (r \ esid 411 through 412 and (name N or name CA or name C or name O or name CB )) or \ resid 413 or (resid 414 through 416 and (name N or name CA or name C or name O \ or name CB )) or resid 417 or (resid 418 through 419 and (name N or name CA or n \ ame C or name O or name CB )) or resid 420 through 461 or (resid 462 through 463 \ and (name N or name CA or name C or name O or name CB )) or resid 464 through 4 \ 72 or (resid 473 and (name N or name CA or name C or name O or name CB )) or res \ id 474 through 480 or (resid 481 and (name N or name CA or name C or name O or n \ ame CB )) or resid 482 through 483 or (resid 484 and (name N or name CA or name \ C or name O or name CB )) or resid 485 through 493 or (resid 494 through 496 and \ (name N or name CA or name C or name O or name CB )) or resid 497 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 07 through 511 or (resid 512 through 515 and (name N or name CA or name C or nam \ e O or name CB )) or resid 518 through 601)) selection = (chain 'B' and ((resid 9 through 29 and (name N or name CA or name C or name O o \ r name CB )) or resid 30 through 35 or (resid 36 through 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 or (resid 39 and (name N or nam \ e CA or name C or name O or name CB )) or resid 40 through 172 or (resid 173 and \ (name N or name CA or name C or name O or name CB )) or resid 174 through 183 o \ r (resid 184 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 85 through 190 or (resid 191 through 192 and (name N or name CA or name C or nam \ e O or name CB )) or resid 193 through 317 or (resid 318 and (name N or name CA \ or name C or name O or name CB )) or resid 319 through 395 or (resid 396 and (na \ me N or name CA or name C or name O or name CB )) or resid 397 through 403 or (r \ esid 404 through 405 and (name N or name CA or name C or name O or name CB )) or \ resid 406 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 487 or (resid 488 and (name N or name CA or n \ ame C or name O or name CB )) or resid 489 through 497 or (resid 498 and (name N \ or name CA or name C or name O or name CB )) or resid 499 through 511 or (resid \ 512 through 515 and (name N or name CA or name C or name O or name CB )) or res \ id 518 through 601)) selection = (chain 'C' and ((resid 9 through 29 and (name N or name CA or name C or name O o \ r name CB )) or resid 30 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 190 or (resid 191 through 192 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 through 294 \ or (resid 295 through 296 and (name N or name CA or name C or name O or name CB \ )) or resid 297 through 357 or (resid 358 and (name N or name CA or name C or n \ ame O or name CB )) or resid 359 through 394 or (resid 395 through 396 and (name \ N or name CA or name C or name O or name CB )) or resid 397 through 403 or (res \ id 404 through 405 and (name N or name CA or name C or name O or name CB )) or r \ esid 406 through 410 or (resid 411 through 412 and (name N or name CA or name C \ or name O or name CB )) or resid 413 or (resid 414 through 416 and (name N or na \ me CA or name C or name O or name CB )) or resid 417 or (resid 418 through 419 a \ nd (name N or name CA or name C or name O or name CB )) or resid 420 through 421 \ or (resid 422 and (name N or name CA or name C or name O or name CB )) or resid \ 423 through 483 or (resid 484 and (name N or name CA or name C or name O or nam \ e CB )) or resid 485 through 497 or (resid 498 and (name N or name CA or name C \ or name O or name CB )) or resid 499 through 505 or (resid 506 and (name N or na \ me CA or name C or name O or name CB )) or resid 507 through 515 or resid 537 th \ rough 538 or resid 540 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 113 or (resid 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 191 or (resid 192 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 through 202 \ or (resid 203 and (name N or name CA or name C or name O or name CB )) or resid \ 204 through 220 or (resid 221 and (name N or name CA or name C or name O or nam \ e CB )) or resid 222 through 284 or (resid 285 through 286 and (name N or name C \ A or name C or name O or name CB )) or resid 287 through 363 or (resid 364 and ( \ name N or name CA or name C or name O or name CB )) or resid 365 through 383 or \ (resid 384 and (name N or name CA or name C or name O or name CB )) or resid 385 \ through 391 or (resid 392 through 393 and (name N or name CA or name C or name \ O or name CB )) or resid 394 through 471)) selection = (chain 'E' and (resid 8 through 134 or (resid 135 and (name N or name CA or name \ C or name O or name CB )) or resid 136 through 191 or (resid 192 and (name N or \ name CA or name C or name O or name CB )) or resid 193 through 253 or (resid 25 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 255 through \ 291 or (resid 292 and (name N or name CA or name C or name O or name CB )) or re \ sid 293 through 312 or (resid 313 and (name N or name CA or name C or name O or \ name CB )) or resid 314 through 395 or (resid 396 and (name N or name CA or name \ C or name O or name CB )) or resid 397 or (resid 398 and (name N or name CA or \ name C or name O or name CB )) or resid 399 through 447 or (resid 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 through 461 or (resi \ d 462 through 463 and (name N or name CA or name C or name O or name CB )) or re \ sid 464 through 468 or (resid 469 and (name N or name CA or name C or name O or \ name CB )) or resid 470 through 471)) selection = (chain 'F' and (resid 8 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 113 or (resid 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 134 or (resid 135 a \ nd (name N or name CA or name C or name O or name CB )) or resid 136 through 202 \ or (resid 203 and (name N or name CA or name C or name O or name CB )) or resid \ 204 through 220 or (resid 221 and (name N or name CA or name C or name O or nam \ e CB )) or resid 222 through 253 or (resid 254 and (name N or name CA or name C \ or name O or name CB )) or resid 255 through 285 or (resid 286 and (name N or na \ me CA or name C or name O or name CB )) or resid 287 through 288 or (resid 289 a \ nd (name N or name CA or name C or name O or name CB )) or resid 290 through 291 \ or (resid 292 and (name N or name CA or name C or name O or name CB )) or resid \ 293 through 312 or (resid 313 and (name N or name CA or name C or name O or nam \ e CB )) or resid 314 through 331 or (resid 332 and (name N or name CA or name C \ or name O or name CB )) or resid 333 through 363 or (resid 364 and (name N or na \ me CA or name C or name O or name CB )) or resid 365 through 395 or (resid 396 a \ nd (name N or name CA or name C or name O or name CB )) or resid 397 or (resid 3 \ 98 and (name N or name CA or name C or name O or name CB )) or resid 399 through \ 447 or (resid 448 and (name N or name CA or name C or name O or name CB )) or r \ esid 449 through 462 or (resid 463 and (name N or name CA or name C or name O or \ name CB )) or resid 464 through 471)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 28.480 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 0.140 36230 Z= 0.475 Angle : 0.756 11.888 49213 Z= 0.489 Chirality : 0.048 0.426 5827 Planarity : 0.005 0.122 6370 Dihedral : 13.981 89.869 12897 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 1.12 % Allowed : 1.18 % Favored : 97.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.12), residues: 4807 helix: 0.79 (0.10), residues: 2629 sheet: -0.89 (0.21), residues: 534 loop : -0.03 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 365 TYR 0.029 0.001 TYR G 126 PHE 0.072 0.002 PHE C 271 TRP 0.011 0.001 TRP D 201 HIS 0.003 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00708 (36230) covalent geometry : angle 0.75578 (49213) hydrogen bonds : bond 0.14581 ( 2293) hydrogen bonds : angle 6.97933 ( 6627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 936 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 ASN cc_start: 0.8721 (t0) cc_final: 0.8307 (t0) REVERT: A 365 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8759 (mpt-90) REVERT: B 333 LYS cc_start: 0.8593 (mttp) cc_final: 0.8079 (mmtp) REVERT: B 487 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7873 (ttm110) REVERT: C 331 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6747 (tm-30) REVERT: E 255 ASN cc_start: 0.7974 (t0) cc_final: 0.7763 (t0) REVERT: E 340 LYS cc_start: 0.8630 (mttt) cc_final: 0.8393 (mtmm) REVERT: H 17 SER cc_start: 0.8636 (p) cc_final: 0.8306 (p) REVERT: H 48 ASP cc_start: 0.8400 (p0) cc_final: 0.8190 (p0) REVERT: H 83 ASN cc_start: 0.8529 (t0) cc_final: 0.8170 (t0) REVERT: H 96 LYS cc_start: 0.9133 (mmtm) cc_final: 0.8112 (mmmm) REVERT: b 66 LYS cc_start: 0.9427 (mmtt) cc_final: 0.9192 (tppt) REVERT: b 109 SER cc_start: 0.9420 (t) cc_final: 0.8527 (p) REVERT: b 115 ARG cc_start: 0.9201 (tpp-160) cc_final: 0.8958 (tpp-160) REVERT: b 160 LEU cc_start: 0.9360 (tt) cc_final: 0.9106 (tm) REVERT: d 281 LYS cc_start: 0.9647 (tppt) cc_final: 0.9401 (tptp) REVERT: d 366 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8844 (tm-30) REVERT: 2 75 MET cc_start: 0.7038 (ttp) cc_final: 0.6730 (ttt) REVERT: 3 20 ILE cc_start: 0.7311 (mt) cc_final: 0.6889 (mm) REVERT: 6 20 ILE cc_start: 0.7726 (mt) cc_final: 0.7423 (mm) REVERT: 1 20 ILE cc_start: 0.6711 (mt) cc_final: 0.6224 (mt) REVERT: 1 79 VAL cc_start: 0.6034 (m) cc_final: 0.5594 (m) outliers start: 39 outliers final: 8 residues processed: 957 average time/residue: 0.5410 time to fit residues: 636.6636 Evaluate side-chains 589 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 580 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain b residue 85 TYR Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain 6 residue 43 ILE Chi-restraints excluded: chain 7 residue 77 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 90 GLN A 188 ASN B 188 ASN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 399 GLN C 453 GLN E 175 ASN F 400 GLN G 52 ASN G 291 GLN H 44 GLN H 119 GLN b 136 GLN d 104 GLN 2 37 ASN 5 6 ASN 6 6 ASN 6 37 ASN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 37 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061190 restraints weight = 90011.405| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.89 r_work: 0.2656 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 36230 Z= 0.231 Angle : 0.722 14.784 49213 Z= 0.367 Chirality : 0.046 0.299 5827 Planarity : 0.005 0.058 6370 Dihedral : 7.033 78.315 5350 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.80 % Allowed : 13.40 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.12), residues: 4807 helix: 1.30 (0.10), residues: 2611 sheet: -0.71 (0.22), residues: 534 loop : 0.28 (0.17), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 406 TYR 0.048 0.002 TYR 3 68 PHE 0.059 0.002 PHE 6 54 TRP 0.019 0.002 TRP a 218 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00520 (36230) covalent geometry : angle 0.72173 (49213) hydrogen bonds : bond 0.04949 ( 2293) hydrogen bonds : angle 5.19025 ( 6627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 657 time to evaluate : 1.087 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 45 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8331 (pp20) REVERT: A 182 CYS cc_start: 0.9312 (m) cc_final: 0.9068 (m) REVERT: A 335 ASN cc_start: 0.9397 (t0) cc_final: 0.9095 (t0) REVERT: A 356 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8836 (mt-10) REVERT: A 369 ASN cc_start: 0.9419 (t0) cc_final: 0.8999 (t0) REVERT: A 402 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 495 GLU cc_start: 0.9342 (tp30) cc_final: 0.9103 (tp30) REVERT: B 356 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: B 369 ASN cc_start: 0.9066 (t0) cc_final: 0.8837 (t0) REVERT: B 400 TYR cc_start: 0.8575 (t80) cc_final: 0.7950 (t80) REVERT: B 401 ARG cc_start: 0.9441 (tpp-160) cc_final: 0.9124 (mmm-85) REVERT: B 487 ARG cc_start: 0.8931 (mtm180) cc_final: 0.8431 (mtm110) REVERT: B 498 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9158 (mm-30) REVERT: C 45 GLU cc_start: 0.8664 (pp20) cc_final: 0.8361 (pp20) REVERT: C 331 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 335 ASN cc_start: 0.9164 (t0) cc_final: 0.8779 (t0) REVERT: C 432 LYS cc_start: 0.9068 (mttt) cc_final: 0.8799 (mttp) REVERT: C 509 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9052 (mtmm) REVERT: D 67 MET cc_start: 0.9505 (mmm) cc_final: 0.9267 (mmm) REVERT: E 67 MET cc_start: 0.9394 (mmm) cc_final: 0.8604 (mmm) REVERT: E 222 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: E 255 ASN cc_start: 0.8538 (t0) cc_final: 0.8322 (t0) REVERT: E 273 MET cc_start: 0.9459 (mtp) cc_final: 0.9186 (mtt) REVERT: E 381 ASP cc_start: 0.9075 (m-30) cc_final: 0.8869 (m-30) REVERT: E 409 GLU cc_start: 0.9382 (tt0) cc_final: 0.9102 (pt0) REVERT: E 425 GLN cc_start: 0.8793 (mp10) cc_final: 0.8548 (mp10) REVERT: F 67 MET cc_start: 0.9275 (mmm) cc_final: 0.9042 (mmp) REVERT: F 199 ASP cc_start: 0.9093 (m-30) cc_final: 0.8872 (t0) REVERT: F 279 TYR cc_start: 0.8854 (m-80) cc_final: 0.8622 (m-80) REVERT: F 347 ASP cc_start: 0.9375 (t0) cc_final: 0.8997 (t0) REVERT: G 122 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8904 (mmtp) REVERT: H 7 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7797 (mm-30) REVERT: H 14 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7595 (tm-30) REVERT: H 26 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7455 (tpp80) REVERT: H 31 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8190 (mp0) REVERT: H 48 ASP cc_start: 0.8831 (p0) cc_final: 0.7969 (t0) REVERT: H 83 ASN cc_start: 0.9107 (t0) cc_final: 0.8835 (t0) REVERT: b 63 MET cc_start: 0.8405 (ttp) cc_final: 0.8128 (tmm) REVERT: b 66 LYS cc_start: 0.9230 (mmtt) cc_final: 0.9023 (tmmt) REVERT: b 115 ARG cc_start: 0.9339 (tpp-160) cc_final: 0.9138 (tpp-160) REVERT: d 53 ASP cc_start: 0.9790 (t0) cc_final: 0.9529 (m-30) REVERT: d 281 LYS cc_start: 0.9641 (tppt) cc_final: 0.9289 (tptp) REVERT: d 366 GLU cc_start: 0.9439 (mm-30) cc_final: 0.8994 (tm-30) REVERT: 2 54 PHE cc_start: 0.7170 (m-10) cc_final: 0.6944 (m-10) REVERT: 3 39 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9083 (tp) REVERT: 3 56 PRO cc_start: 0.8809 (Cg_exo) cc_final: 0.8434 (Cg_endo) REVERT: 3 75 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8703 (ttm) REVERT: 4 6 ASN cc_start: 0.8380 (p0) cc_final: 0.7575 (t0) REVERT: 4 21 MET cc_start: 0.8037 (mmp) cc_final: 0.7760 (mmp) REVERT: 4 54 PHE cc_start: 0.8259 (p90) cc_final: 0.7927 (p90) REVERT: 4 58 PHE cc_start: 0.8706 (m-10) cc_final: 0.8326 (m-80) REVERT: 5 77 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7988 (pp) REVERT: 5 78 PHE cc_start: 0.7848 (m-80) cc_final: 0.7584 (m-80) REVERT: 6 37 ASN cc_start: 0.9188 (t0) cc_final: 0.8514 (m110) REVERT: 6 43 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8480 (mm) REVERT: 7 37 ASN cc_start: 0.9146 (t0) cc_final: 0.8923 (t0) REVERT: 7 50 GLN cc_start: 0.8547 (tm130) cc_final: 0.8033 (tm130) REVERT: 7 54 PHE cc_start: 0.9204 (m-80) cc_final: 0.8996 (m-80) REVERT: 7 75 MET cc_start: 0.8142 (tmm) cc_final: 0.7910 (tmm) REVERT: 7 78 PHE cc_start: 0.8029 (m-80) cc_final: 0.7696 (m-80) REVERT: 8 14 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7827 (tm) REVERT: 8 74 PHE cc_start: 0.9041 (t80) cc_final: 0.8767 (t80) REVERT: 8 78 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: 9 78 PHE cc_start: 0.8129 (m-80) cc_final: 0.7136 (m-80) REVERT: a 66 TRP cc_start: 0.8748 (m100) cc_final: 0.8505 (m100) REVERT: a 73 MET cc_start: 0.9513 (tpp) cc_final: 0.9044 (ttm) REVERT: a 105 TRP cc_start: 0.7423 (m100) cc_final: 0.6855 (m100) REVERT: a 106 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8597 (mt) REVERT: a 130 ASP cc_start: 0.7306 (t0) cc_final: 0.7102 (t0) REVERT: a 179 LEU cc_start: 0.9495 (mm) cc_final: 0.9292 (pp) REVERT: a 181 LYS cc_start: 0.9331 (mttt) cc_final: 0.8924 (mmtt) REVERT: a 222 ASP cc_start: 0.8687 (m-30) cc_final: 0.8246 (m-30) REVERT: a 240 TYR cc_start: 0.9528 (m-10) cc_final: 0.9113 (m-10) REVERT: a 245 MET cc_start: 0.9099 (mtp) cc_final: 0.8784 (mpp) REVERT: 1 45 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7675 (mmm-85) REVERT: 1 69 PHE cc_start: 0.7758 (m-80) cc_final: 0.7471 (m-80) outliers start: 132 outliers final: 26 residues processed: 719 average time/residue: 0.5089 time to fit residues: 457.0072 Evaluate side-chains 620 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 581 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 26 ARG Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 3 residue 82 THR Chi-restraints excluded: chain 4 residue 59 ILE Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 6 residue 43 ILE Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 9 residue 70 ILE Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain 1 residue 40 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 97 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 367 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 378 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 chunk 349 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 335 ASN D 403 ASN G 37 GLN G 52 ASN G 93 ASN G 131 GLN G 291 GLN G 301 ASN H 44 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 266 ASN 2 37 ASN ** 3 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 6 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061795 restraints weight = 89816.838| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.91 r_work: 0.2685 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 36230 Z= 0.164 Angle : 0.660 12.354 49213 Z= 0.334 Chirality : 0.045 0.487 5827 Planarity : 0.004 0.073 6370 Dihedral : 6.588 85.977 5338 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.46 % Allowed : 15.53 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.12), residues: 4807 helix: 1.52 (0.10), residues: 2617 sheet: -0.61 (0.23), residues: 520 loop : 0.25 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 74 TYR 0.023 0.002 TYR a 145 PHE 0.053 0.002 PHE 8 58 TRP 0.015 0.001 TRP a 212 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00391 (36230) covalent geometry : angle 0.66048 (49213) hydrogen bonds : bond 0.04510 ( 2293) hydrogen bonds : angle 4.91468 ( 6627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 641 time to evaluate : 1.443 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 45 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8346 (pp20) REVERT: A 182 CYS cc_start: 0.9304 (m) cc_final: 0.9033 (m) REVERT: A 211 GLN cc_start: 0.8679 (mt0) cc_final: 0.8430 (mt0) REVERT: A 225 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8500 (mp0) REVERT: A 335 ASN cc_start: 0.9393 (t0) cc_final: 0.9103 (t0) REVERT: A 369 ASN cc_start: 0.9346 (t0) cc_final: 0.8788 (t0) REVERT: A 402 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 443 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: A 468 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8564 (pp20) REVERT: B 333 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8468 (mtpp) REVERT: B 356 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 369 ASN cc_start: 0.9121 (t0) cc_final: 0.8836 (t0) REVERT: B 400 TYR cc_start: 0.8539 (t80) cc_final: 0.7993 (t80) REVERT: B 404 GLU cc_start: 0.8461 (pt0) cc_final: 0.8076 (pt0) REVERT: B 448 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9137 (mp) REVERT: B 487 ARG cc_start: 0.8903 (mtm180) cc_final: 0.8692 (ttm110) REVERT: C 45 GLU cc_start: 0.8722 (pp20) cc_final: 0.8406 (pp20) REVERT: C 55 LEU cc_start: 0.9473 (mt) cc_final: 0.9246 (mm) REVERT: C 70 ASP cc_start: 0.8618 (t0) cc_final: 0.8324 (t0) REVERT: C 90 GLN cc_start: 0.9233 (mt0) cc_final: 0.8493 (pp30) REVERT: C 331 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7748 (tm-30) REVERT: C 335 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8456 (t160) REVERT: C 402 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8548 (tm-30) REVERT: D 67 MET cc_start: 0.9575 (mmm) cc_final: 0.9192 (mmm) REVERT: D 78 GLU cc_start: 0.9235 (tt0) cc_final: 0.8753 (tm-30) REVERT: D 203 GLU cc_start: 0.8739 (tp30) cc_final: 0.8370 (tp30) REVERT: D 328 ASP cc_start: 0.8622 (m-30) cc_final: 0.8350 (m-30) REVERT: D 335 ARG cc_start: 0.9019 (mtp-110) cc_final: 0.8748 (tpp80) REVERT: E 67 MET cc_start: 0.9465 (mmm) cc_final: 0.8653 (mmm) REVERT: E 222 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: E 255 ASN cc_start: 0.8392 (t0) cc_final: 0.8082 (t0) REVERT: E 273 MET cc_start: 0.9438 (mtp) cc_final: 0.9165 (mtt) REVERT: E 381 ASP cc_start: 0.9117 (m-30) cc_final: 0.8858 (m-30) REVERT: E 425 GLN cc_start: 0.8840 (mp10) cc_final: 0.8614 (mp10) REVERT: F 78 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: F 279 TYR cc_start: 0.8857 (m-80) cc_final: 0.8647 (m-80) REVERT: F 347 ASP cc_start: 0.9428 (t0) cc_final: 0.9024 (t0) REVERT: F 422 PHE cc_start: 0.9175 (m-80) cc_final: 0.8610 (m-80) REVERT: F 444 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9174 (mtmm) REVERT: G 85 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: H 7 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7706 (mm-30) REVERT: H 26 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7492 (tpp80) REVERT: H 47 ASP cc_start: 0.9198 (m-30) cc_final: 0.8833 (p0) REVERT: H 48 ASP cc_start: 0.8895 (p0) cc_final: 0.7923 (t0) REVERT: H 83 ASN cc_start: 0.9085 (t0) cc_final: 0.8816 (t0) REVERT: b 63 MET cc_start: 0.8591 (ttp) cc_final: 0.8316 (tmm) REVERT: b 66 LYS cc_start: 0.9267 (mmtt) cc_final: 0.9002 (tmmt) REVERT: d 53 ASP cc_start: 0.9687 (t0) cc_final: 0.9464 (m-30) REVERT: d 68 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8364 (pp20) REVERT: d 281 LYS cc_start: 0.9603 (tppt) cc_final: 0.9236 (tptp) REVERT: d 366 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8962 (tm-30) REVERT: 4 6 ASN cc_start: 0.8389 (p0) cc_final: 0.7624 (t0) REVERT: 4 21 MET cc_start: 0.8455 (mmp) cc_final: 0.8161 (mmp) REVERT: 4 75 MET cc_start: 0.9131 (tmm) cc_final: 0.8555 (ppp) REVERT: 4 78 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6864 (t80) REVERT: 5 14 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6191 (tm) REVERT: 5 50 GLN cc_start: 0.8773 (pp30) cc_final: 0.8153 (pp30) REVERT: 5 68 TYR cc_start: 0.7633 (t80) cc_final: 0.7175 (t80) REVERT: 6 6 ASN cc_start: 0.9067 (m-40) cc_final: 0.8620 (p0) REVERT: 6 19 LEU cc_start: 0.9220 (mm) cc_final: 0.8962 (tt) REVERT: 6 37 ASN cc_start: 0.9308 (t0) cc_final: 0.8573 (m110) REVERT: 6 43 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8437 (mm) REVERT: 6 54 PHE cc_start: 0.9035 (m-80) cc_final: 0.8486 (m-80) REVERT: 6 78 PHE cc_start: 0.8837 (m-10) cc_final: 0.8451 (m-10) REVERT: 7 50 GLN cc_start: 0.8616 (tm130) cc_final: 0.7934 (tm130) REVERT: 7 54 PHE cc_start: 0.9250 (m-80) cc_final: 0.8833 (m-80) REVERT: 7 80 PHE cc_start: 0.8645 (m-10) cc_final: 0.8213 (m-80) REVERT: 7 82 THR cc_start: 0.8123 (m) cc_final: 0.7797 (m) REVERT: 8 68 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8543 (t80) REVERT: 8 69 PHE cc_start: 0.9101 (m-10) cc_final: 0.8779 (m-10) REVERT: 8 78 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: 9 69 PHE cc_start: 0.9197 (m-80) cc_final: 0.8970 (m-80) REVERT: 9 74 PHE cc_start: 0.8137 (t80) cc_final: 0.7587 (t80) REVERT: 9 75 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9013 (mtp) REVERT: 9 78 PHE cc_start: 0.8186 (m-80) cc_final: 0.7917 (m-80) REVERT: a 66 TRP cc_start: 0.8838 (m100) cc_final: 0.8620 (m100) REVERT: a 105 TRP cc_start: 0.7491 (m100) cc_final: 0.6799 (m100) REVERT: a 106 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8532 (mt) REVERT: a 132 ASN cc_start: 0.7805 (m-40) cc_final: 0.7433 (m-40) REVERT: a 179 LEU cc_start: 0.9500 (mm) cc_final: 0.9273 (pp) REVERT: a 181 LYS cc_start: 0.9314 (mttt) cc_final: 0.9058 (mmtt) REVERT: a 222 ASP cc_start: 0.8863 (m-30) cc_final: 0.8456 (m-30) REVERT: a 223 LEU cc_start: 0.9214 (mt) cc_final: 0.8992 (mt) REVERT: a 240 TYR cc_start: 0.9498 (m-10) cc_final: 0.9023 (m-10) REVERT: a 245 MET cc_start: 0.9132 (mtp) cc_final: 0.8616 (mpp) REVERT: 1 21 MET cc_start: 0.7910 (mmp) cc_final: 0.7476 (mmt) REVERT: 1 69 PHE cc_start: 0.7826 (m-10) cc_final: 0.7564 (m-10) REVERT: 1 71 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8007 (t0) outliers start: 120 outliers final: 31 residues processed: 698 average time/residue: 0.5365 time to fit residues: 466.5875 Evaluate side-chains 624 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 573 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 26 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain 3 residue 53 LEU Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 82 THR Chi-restraints excluded: chain 4 residue 78 PHE Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 6 residue 43 ILE Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 8 residue 21 MET Chi-restraints excluded: chain 8 residue 68 TYR Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 9 residue 75 MET Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 140 PHE Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain 1 residue 9 ILE Chi-restraints excluded: chain 1 residue 40 ILE Chi-restraints excluded: chain 1 residue 71 ASN Chi-restraints excluded: chain 1 residue 75 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 195 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 374 optimal weight: 0.5980 chunk 447 optimal weight: 10.0000 chunk 425 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 452 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 414 optimal weight: 0.0370 chunk 282 optimal weight: 0.9980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN G 65 HIS G 291 GLN G 301 ASN H 44 GLN 2 37 ASN ** 3 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 71 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.096426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.062035 restraints weight = 89572.701| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.88 r_work: 0.2686 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 36230 Z= 0.158 Angle : 0.660 12.849 49213 Z= 0.331 Chirality : 0.045 0.516 5827 Planarity : 0.004 0.053 6370 Dihedral : 6.355 85.427 5336 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.28 % Allowed : 16.94 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.12), residues: 4807 helix: 1.54 (0.10), residues: 2626 sheet: -0.62 (0.23), residues: 515 loop : 0.26 (0.17), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 115 TYR 0.025 0.002 TYR A 400 PHE 0.048 0.002 PHE 5 69 TRP 0.039 0.001 TRP H 16 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00367 (36230) covalent geometry : angle 0.65990 (49213) hydrogen bonds : bond 0.04390 ( 2293) hydrogen bonds : angle 4.85380 ( 6627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 614 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8438 (pp20) REVERT: A 182 CYS cc_start: 0.9347 (m) cc_final: 0.9088 (m) REVERT: A 225 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8602 (mp0) REVERT: A 335 ASN cc_start: 0.9526 (t0) cc_final: 0.9067 (t0) REVERT: A 402 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 443 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8612 (mt-10) REVERT: A 468 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8613 (pp20) REVERT: B 333 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8676 (mtmm) REVERT: B 356 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: B 369 ASN cc_start: 0.9096 (t0) cc_final: 0.8763 (t0) REVERT: B 400 TYR cc_start: 0.8394 (t80) cc_final: 0.7537 (t80) REVERT: B 401 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8561 (mmm-85) REVERT: B 487 ARG cc_start: 0.8936 (mtm180) cc_final: 0.8702 (ttm110) REVERT: C 45 GLU cc_start: 0.8799 (pp20) cc_final: 0.8465 (pp20) REVERT: C 55 LEU cc_start: 0.9504 (mt) cc_final: 0.9258 (mm) REVERT: C 70 ASP cc_start: 0.8559 (t0) cc_final: 0.8284 (t0) REVERT: C 90 GLN cc_start: 0.9257 (mt0) cc_final: 0.8540 (pp30) REVERT: C 331 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7719 (tm-30) REVERT: C 335 ASN cc_start: 0.9114 (t0) cc_final: 0.8567 (t160) REVERT: C 336 ASP cc_start: 0.9234 (t0) cc_final: 0.8891 (t0) REVERT: C 402 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8534 (tm-30) REVERT: C 509 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8941 (mtmm) REVERT: D 67 MET cc_start: 0.9566 (mmm) cc_final: 0.9205 (mmm) REVERT: D 78 GLU cc_start: 0.9224 (tt0) cc_final: 0.8810 (tm-30) REVERT: D 203 GLU cc_start: 0.8749 (tp30) cc_final: 0.8348 (tp30) REVERT: D 328 ASP cc_start: 0.8624 (m-30) cc_final: 0.8308 (m-30) REVERT: D 335 ARG cc_start: 0.9055 (mtp-110) cc_final: 0.8787 (tpp80) REVERT: E 45 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8886 (pp) REVERT: E 67 MET cc_start: 0.9485 (mmm) cc_final: 0.8611 (mmm) REVERT: E 273 MET cc_start: 0.9430 (mtp) cc_final: 0.9186 (mtt) REVERT: E 347 ASP cc_start: 0.9158 (t0) cc_final: 0.8527 (t0) REVERT: E 381 ASP cc_start: 0.9093 (m-30) cc_final: 0.8778 (m-30) REVERT: E 425 GLN cc_start: 0.8864 (mp10) cc_final: 0.8642 (mp10) REVERT: F 78 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8640 (tm-30) REVERT: F 289 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8193 (tp30) REVERT: F 347 ASP cc_start: 0.9470 (t0) cc_final: 0.9100 (t0) REVERT: F 422 PHE cc_start: 0.9163 (m-80) cc_final: 0.8797 (m-80) REVERT: F 444 LYS cc_start: 0.9411 (mtmt) cc_final: 0.9165 (mtmm) REVERT: G 85 ASP cc_start: 0.8829 (p0) cc_final: 0.8159 (m-30) REVERT: G 284 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8051 (tm-30) REVERT: H 7 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7720 (mm-30) REVERT: H 39 ILE cc_start: 0.9142 (pt) cc_final: 0.8923 (pp) REVERT: H 47 ASP cc_start: 0.9243 (m-30) cc_final: 0.8909 (p0) REVERT: H 48 ASP cc_start: 0.8939 (p0) cc_final: 0.8099 (t0) REVERT: H 82 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8261 (mm-30) REVERT: H 83 ASN cc_start: 0.9150 (t0) cc_final: 0.8917 (t0) REVERT: b 35 LEU cc_start: 0.8020 (pp) cc_final: 0.7771 (pp) REVERT: b 63 MET cc_start: 0.8537 (ttp) cc_final: 0.8116 (tmm) REVERT: b 66 LYS cc_start: 0.9227 (mmtt) cc_final: 0.8958 (tmmt) REVERT: b 158 ARG cc_start: 0.9561 (mmm-85) cc_final: 0.8802 (tpp80) REVERT: d 53 ASP cc_start: 0.9769 (t0) cc_final: 0.9515 (m-30) REVERT: d 55 ASP cc_start: 0.9389 (t0) cc_final: 0.9067 (m-30) REVERT: d 68 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7861 (pp20) REVERT: d 281 LYS cc_start: 0.9616 (tppt) cc_final: 0.9244 (tptp) REVERT: d 366 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8978 (tm-30) REVERT: 3 75 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8565 (ppp) REVERT: 4 6 ASN cc_start: 0.8346 (p0) cc_final: 0.7608 (t0) REVERT: 4 21 MET cc_start: 0.8469 (mmp) cc_final: 0.8195 (mmp) REVERT: 4 58 PHE cc_start: 0.8852 (m-10) cc_final: 0.8639 (m-10) REVERT: 4 71 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.7101 (m-40) REVERT: 4 75 MET cc_start: 0.9111 (tmm) cc_final: 0.8361 (ppp) REVERT: 5 50 GLN cc_start: 0.8888 (pp30) cc_final: 0.8649 (tm-30) REVERT: 6 6 ASN cc_start: 0.9046 (m-40) cc_final: 0.8611 (p0) REVERT: 6 37 ASN cc_start: 0.9277 (t0) cc_final: 0.8622 (m110) REVERT: 6 54 PHE cc_start: 0.9000 (m-80) cc_final: 0.8437 (m-80) REVERT: 7 37 ASN cc_start: 0.9035 (t0) cc_final: 0.8500 (m-40) REVERT: 7 50 GLN cc_start: 0.8609 (tm130) cc_final: 0.8058 (tm130) REVERT: 7 54 PHE cc_start: 0.9260 (m-80) cc_final: 0.8673 (m-80) REVERT: 7 75 MET cc_start: 0.8050 (tmm) cc_final: 0.7793 (tmm) REVERT: 7 80 PHE cc_start: 0.8621 (m-10) cc_final: 0.8172 (m-80) REVERT: 7 82 THR cc_start: 0.7896 (m) cc_final: 0.7676 (m) REVERT: 8 58 PHE cc_start: 0.9091 (m-80) cc_final: 0.8879 (m-80) REVERT: 8 68 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8763 (t80) REVERT: 8 69 PHE cc_start: 0.9078 (m-10) cc_final: 0.8683 (m-10) REVERT: 8 74 PHE cc_start: 0.8907 (t80) cc_final: 0.8616 (t80) REVERT: 9 69 PHE cc_start: 0.9302 (m-10) cc_final: 0.9071 (m-80) REVERT: 9 74 PHE cc_start: 0.8049 (t80) cc_final: 0.7755 (t80) REVERT: a 66 TRP cc_start: 0.8878 (m100) cc_final: 0.8629 (m100) REVERT: a 72 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8208 (tp-100) REVERT: a 73 MET cc_start: 0.9485 (tpp) cc_final: 0.9039 (ttt) REVERT: a 105 TRP cc_start: 0.7622 (m100) cc_final: 0.6781 (m100) REVERT: a 106 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8821 (mt) REVERT: a 130 ASP cc_start: 0.7012 (t0) cc_final: 0.6806 (t0) REVERT: a 181 LYS cc_start: 0.9383 (mttt) cc_final: 0.9142 (mmtt) REVERT: a 222 ASP cc_start: 0.8823 (m-30) cc_final: 0.8430 (m-30) REVERT: a 223 LEU cc_start: 0.9126 (mt) cc_final: 0.8899 (mt) REVERT: a 240 TYR cc_start: 0.9470 (m-10) cc_final: 0.9072 (m-10) REVERT: 1 69 PHE cc_start: 0.7901 (m-10) cc_final: 0.7654 (m-10) outliers start: 114 outliers final: 29 residues processed: 672 average time/residue: 0.5163 time to fit residues: 431.5842 Evaluate side-chains 598 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 555 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 82 THR Chi-restraints excluded: chain 4 residue 71 ASN Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 8 residue 68 TYR Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain 9 residue 21 MET Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain 1 residue 9 ILE Chi-restraints excluded: chain 1 residue 40 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 433 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 320 optimal weight: 8.9990 chunk 324 optimal weight: 1.9990 chunk 368 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 339 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN B 53 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN G 37 GLN G 52 ASN G 93 ASN G 131 GLN G 291 GLN H 44 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 ASN ** 3 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 71 ASN ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 ASN a 166 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061322 restraints weight = 89778.424| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.88 r_work: 0.2661 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 36230 Z= 0.180 Angle : 0.676 16.066 49213 Z= 0.335 Chirality : 0.045 0.294 5827 Planarity : 0.004 0.052 6370 Dihedral : 6.182 81.645 5334 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.97 % Allowed : 18.15 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.12), residues: 4807 helix: 1.57 (0.10), residues: 2616 sheet: -0.64 (0.22), residues: 530 loop : 0.34 (0.17), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 7 52 TYR 0.025 0.002 TYR 8 68 PHE 0.046 0.002 PHE 5 78 TRP 0.029 0.001 TRP a 212 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00421 (36230) covalent geometry : angle 0.67573 (49213) hydrogen bonds : bond 0.04321 ( 2293) hydrogen bonds : angle 4.80194 ( 6627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 588 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8386 (pp20) REVERT: A 182 CYS cc_start: 0.9372 (m) cc_final: 0.9092 (m) REVERT: A 225 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8646 (mp0) REVERT: A 335 ASN cc_start: 0.9558 (t0) cc_final: 0.9073 (t0) REVERT: A 356 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8859 (mt-10) REVERT: A 402 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 443 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: A 468 GLU cc_start: 0.8828 (pt0) cc_final: 0.8601 (pp20) REVERT: B 333 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8673 (mtmm) REVERT: B 356 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: B 369 ASN cc_start: 0.9081 (t0) cc_final: 0.8721 (t0) REVERT: B 487 ARG cc_start: 0.8970 (mtm180) cc_final: 0.8697 (ttm110) REVERT: C 45 GLU cc_start: 0.8831 (pp20) cc_final: 0.8530 (pp20) REVERT: C 55 LEU cc_start: 0.9511 (mt) cc_final: 0.9174 (mm) REVERT: C 90 GLN cc_start: 0.9252 (mt0) cc_final: 0.8560 (pp30) REVERT: C 331 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 335 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8558 (t160) REVERT: C 336 ASP cc_start: 0.9210 (t0) cc_final: 0.8852 (t0) REVERT: C 402 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8504 (tm-30) REVERT: C 509 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8928 (mtmm) REVERT: D 67 MET cc_start: 0.9599 (mmm) cc_final: 0.9099 (mmm) REVERT: D 78 GLU cc_start: 0.9251 (tt0) cc_final: 0.8819 (tm-30) REVERT: D 185 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9022 (t) REVERT: D 203 GLU cc_start: 0.8766 (tp30) cc_final: 0.8336 (tp30) REVERT: D 287 MET cc_start: 0.9289 (tpp) cc_final: 0.8992 (tpp) REVERT: D 335 ARG cc_start: 0.9065 (mtp-110) cc_final: 0.8745 (tpp80) REVERT: D 383 GLN cc_start: 0.8831 (tp40) cc_final: 0.8520 (mm110) REVERT: E 45 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8826 (pp) REVERT: E 67 MET cc_start: 0.9523 (mmm) cc_final: 0.8830 (mmm) REVERT: E 222 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: E 226 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9035 (t) REVERT: E 273 MET cc_start: 0.9430 (mtp) cc_final: 0.9175 (mtt) REVERT: E 347 ASP cc_start: 0.9164 (t0) cc_final: 0.8538 (t0) REVERT: E 381 ASP cc_start: 0.9065 (m-30) cc_final: 0.8788 (m-30) REVERT: E 425 GLN cc_start: 0.8857 (mp10) cc_final: 0.8503 (mp10) REVERT: F 289 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8604 (tp30) REVERT: F 305 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8859 (ttp) REVERT: F 314 ASP cc_start: 0.9106 (t0) cc_final: 0.8863 (t0) REVERT: F 347 ASP cc_start: 0.9483 (t0) cc_final: 0.9061 (t0) REVERT: F 422 PHE cc_start: 0.9128 (m-80) cc_final: 0.8732 (m-80) REVERT: F 444 LYS cc_start: 0.9356 (mtmt) cc_final: 0.9147 (mtmp) REVERT: G 85 ASP cc_start: 0.8883 (p0) cc_final: 0.8132 (m-30) REVERT: G 284 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8157 (tm-30) REVERT: H 7 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7524 (mm-30) REVERT: H 39 ILE cc_start: 0.9178 (pt) cc_final: 0.8950 (pp) REVERT: H 47 ASP cc_start: 0.9236 (m-30) cc_final: 0.8915 (p0) REVERT: H 48 ASP cc_start: 0.8922 (p0) cc_final: 0.8123 (t0) REVERT: H 83 ASN cc_start: 0.9139 (t0) cc_final: 0.8898 (t0) REVERT: b 53 ILE cc_start: 0.8267 (mm) cc_final: 0.7918 (tp) REVERT: b 55 LYS cc_start: 0.9205 (mmtm) cc_final: 0.8969 (mmtm) REVERT: b 63 MET cc_start: 0.8523 (ttp) cc_final: 0.8107 (tmm) REVERT: b 66 LYS cc_start: 0.9223 (mmtt) cc_final: 0.8927 (tmmt) REVERT: b 158 ARG cc_start: 0.9582 (mmm-85) cc_final: 0.8815 (tpp80) REVERT: d 53 ASP cc_start: 0.9757 (t0) cc_final: 0.9491 (m-30) REVERT: d 55 ASP cc_start: 0.9382 (t0) cc_final: 0.9058 (m-30) REVERT: d 281 LYS cc_start: 0.9635 (tppt) cc_final: 0.9246 (tptp) REVERT: d 366 GLU cc_start: 0.9460 (mm-30) cc_final: 0.8978 (tm-30) REVERT: 2 71 ASN cc_start: 0.8494 (t0) cc_final: 0.8221 (t0) REVERT: 3 65 GLU cc_start: 0.9054 (tt0) cc_final: 0.8574 (tm-30) REVERT: 4 6 ASN cc_start: 0.8336 (p0) cc_final: 0.7619 (t0) REVERT: 4 54 PHE cc_start: 0.8031 (p90) cc_final: 0.7754 (p90) REVERT: 4 58 PHE cc_start: 0.8793 (m-10) cc_final: 0.8495 (m-10) REVERT: 5 52 ARG cc_start: 0.8358 (mpt-90) cc_final: 0.8056 (ptp-170) REVERT: 6 6 ASN cc_start: 0.9032 (m-40) cc_final: 0.8647 (p0) REVERT: 6 37 ASN cc_start: 0.9243 (t0) cc_final: 0.8617 (m110) REVERT: 6 54 PHE cc_start: 0.8998 (m-80) cc_final: 0.8403 (m-80) REVERT: 7 20 ILE cc_start: 0.9172 (mm) cc_final: 0.8810 (mm) REVERT: 7 37 ASN cc_start: 0.9065 (t0) cc_final: 0.8478 (m110) REVERT: 7 50 GLN cc_start: 0.8618 (tm130) cc_final: 0.8047 (tm130) REVERT: 7 54 PHE cc_start: 0.9281 (m-80) cc_final: 0.8752 (m-80) REVERT: 7 78 PHE cc_start: 0.8044 (m-10) cc_final: 0.7649 (m-80) REVERT: 7 80 PHE cc_start: 0.8598 (m-10) cc_final: 0.8142 (m-80) REVERT: 8 39 LEU cc_start: 0.9392 (pp) cc_final: 0.9185 (pp) REVERT: 8 58 PHE cc_start: 0.9098 (m-80) cc_final: 0.8691 (m-80) REVERT: 8 68 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8708 (t80) REVERT: 8 69 PHE cc_start: 0.8996 (m-10) cc_final: 0.8507 (m-10) REVERT: 8 74 PHE cc_start: 0.8856 (t80) cc_final: 0.8555 (t80) REVERT: 9 52 ARG cc_start: 0.8535 (tmm-80) cc_final: 0.8300 (ttt180) REVERT: 9 69 PHE cc_start: 0.9188 (m-10) cc_final: 0.8876 (m-80) REVERT: 9 74 PHE cc_start: 0.8005 (t80) cc_final: 0.7675 (t80) REVERT: 9 78 PHE cc_start: 0.8273 (m-80) cc_final: 0.7931 (m-80) REVERT: a 73 MET cc_start: 0.9549 (tpp) cc_final: 0.9107 (ttt) REVERT: a 74 ARG cc_start: 0.9368 (tmt-80) cc_final: 0.9126 (tpm170) REVERT: a 105 TRP cc_start: 0.7495 (m100) cc_final: 0.6654 (m100) REVERT: a 106 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8751 (mt) REVERT: a 181 LYS cc_start: 0.9319 (mttt) cc_final: 0.9052 (mmtp) REVERT: a 222 ASP cc_start: 0.8822 (m-30) cc_final: 0.8482 (m-30) REVERT: a 240 TYR cc_start: 0.9433 (m-10) cc_final: 0.9116 (m-10) REVERT: 1 52 ARG cc_start: 0.8427 (ptt-90) cc_final: 0.7917 (ptt90) outliers start: 103 outliers final: 38 residues processed: 643 average time/residue: 0.5168 time to fit residues: 413.8668 Evaluate side-chains 595 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 544 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 82 THR Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 57 PHE Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 68 TYR Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain 1 residue 9 ILE Chi-restraints excluded: chain 1 residue 40 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 176 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 415 optimal weight: 6.9990 chunk 387 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 430 optimal weight: 6.9990 chunk 414 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 305 HIS B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 370 GLN G 37 GLN G 52 ASN G 131 GLN G 291 GLN H 44 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 ASN d 266 ASN 2 37 ASN 3 37 ASN ** 7 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.058457 restraints weight = 90632.689| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.86 r_work: 0.2648 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 36230 Z= 0.236 Angle : 0.701 18.033 49213 Z= 0.348 Chirality : 0.046 0.461 5827 Planarity : 0.004 0.065 6370 Dihedral : 6.146 80.618 5333 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.31 % Allowed : 19.10 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.12), residues: 4807 helix: 1.60 (0.10), residues: 2617 sheet: -0.70 (0.22), residues: 555 loop : 0.39 (0.17), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG b 115 TYR 0.032 0.002 TYR E 366 PHE 0.050 0.002 PHE 5 78 TRP 0.034 0.002 TRP a 212 HIS 0.004 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00545 (36230) covalent geometry : angle 0.70118 (49213) hydrogen bonds : bond 0.04426 ( 2293) hydrogen bonds : angle 4.80029 ( 6627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 571 time to evaluate : 0.974 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 45 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8383 (pp20) REVERT: A 182 CYS cc_start: 0.9395 (m) cc_final: 0.9120 (m) REVERT: A 225 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8693 (mp0) REVERT: A 335 ASN cc_start: 0.9558 (t0) cc_final: 0.9099 (t0) REVERT: A 356 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8930 (mt-10) REVERT: A 402 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 443 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: A 468 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8677 (pp20) REVERT: B 333 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8780 (mtmm) REVERT: B 356 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: B 369 ASN cc_start: 0.9077 (t0) cc_final: 0.8716 (t0) REVERT: B 413 LEU cc_start: 0.7522 (pt) cc_final: 0.7181 (pt) REVERT: B 448 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9194 (mp) REVERT: B 487 ARG cc_start: 0.8984 (mtm180) cc_final: 0.8701 (ttm110) REVERT: C 45 GLU cc_start: 0.8879 (pp20) cc_final: 0.8625 (pp20) REVERT: C 331 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7758 (tm-30) REVERT: C 335 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8795 (t160) REVERT: C 509 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8990 (mtmm) REVERT: D 67 MET cc_start: 0.9604 (mmm) cc_final: 0.9068 (mmm) REVERT: D 78 GLU cc_start: 0.9273 (tt0) cc_final: 0.8845 (tm-30) REVERT: D 185 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9050 (t) REVERT: D 203 GLU cc_start: 0.8802 (tp30) cc_final: 0.8483 (tp30) REVERT: D 287 MET cc_start: 0.9343 (tpp) cc_final: 0.9070 (tpp) REVERT: D 335 ARG cc_start: 0.9095 (mtp-110) cc_final: 0.8792 (tpp80) REVERT: D 383 GLN cc_start: 0.8949 (tp40) cc_final: 0.8603 (mm110) REVERT: E 45 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8845 (pp) REVERT: E 123 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9173 (mtpp) REVERT: E 158 LEU cc_start: 0.9229 (mp) cc_final: 0.8890 (mt) REVERT: E 222 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: E 273 MET cc_start: 0.9422 (mtp) cc_final: 0.9132 (mtt) REVERT: E 305 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8605 (tpp) REVERT: E 347 ASP cc_start: 0.9178 (t0) cc_final: 0.8550 (t0) REVERT: E 381 ASP cc_start: 0.9054 (m-30) cc_final: 0.8757 (m-30) REVERT: E 425 GLN cc_start: 0.8849 (mp10) cc_final: 0.8513 (mp10) REVERT: F 78 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: F 254 ASP cc_start: 0.8728 (t0) cc_final: 0.8518 (t0) REVERT: F 289 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8180 (tp30) REVERT: F 347 ASP cc_start: 0.9475 (t0) cc_final: 0.8999 (t0) REVERT: F 422 PHE cc_start: 0.9120 (m-80) cc_final: 0.8717 (m-80) REVERT: F 444 LYS cc_start: 0.9364 (mtmt) cc_final: 0.9140 (mtmm) REVERT: G 19 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8751 (ttmm) REVERT: G 284 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8222 (tm-30) REVERT: H 31 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8099 (mm-30) REVERT: H 39 ILE cc_start: 0.9167 (pt) cc_final: 0.8966 (pp) REVERT: H 47 ASP cc_start: 0.9232 (m-30) cc_final: 0.8879 (p0) REVERT: H 48 ASP cc_start: 0.8979 (p0) cc_final: 0.8053 (t0) REVERT: H 82 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8092 (mm-30) REVERT: H 83 ASN cc_start: 0.9117 (t0) cc_final: 0.8912 (t0) REVERT: b 63 MET cc_start: 0.8627 (ttp) cc_final: 0.8197 (tmm) REVERT: b 66 LYS cc_start: 0.9270 (mmtt) cc_final: 0.8943 (tmmt) REVERT: b 158 ARG cc_start: 0.9619 (mmm-85) cc_final: 0.8894 (tpp80) REVERT: d 55 ASP cc_start: 0.9319 (t0) cc_final: 0.8984 (m-30) REVERT: d 68 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7825 (pp20) REVERT: d 281 LYS cc_start: 0.9633 (tppt) cc_final: 0.9228 (tptp) REVERT: d 295 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.9125 (tp40) REVERT: d 366 GLU cc_start: 0.9470 (mm-30) cc_final: 0.8989 (tm-30) REVERT: 3 65 GLU cc_start: 0.9059 (tt0) cc_final: 0.8501 (tm-30) REVERT: 3 75 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8257 (tmm) REVERT: 4 6 ASN cc_start: 0.8353 (p0) cc_final: 0.7673 (t0) REVERT: 4 58 PHE cc_start: 0.8861 (m-10) cc_final: 0.8539 (m-10) REVERT: 4 75 MET cc_start: 0.9400 (tmm) cc_final: 0.8842 (ppp) REVERT: 5 21 MET cc_start: 0.8607 (mmt) cc_final: 0.8342 (mmt) REVERT: 5 52 ARG cc_start: 0.8524 (mpt-90) cc_final: 0.8283 (ptp-170) REVERT: 6 6 ASN cc_start: 0.8954 (m-40) cc_final: 0.8570 (p0) REVERT: 6 37 ASN cc_start: 0.9326 (t0) cc_final: 0.8681 (m-40) REVERT: 6 54 PHE cc_start: 0.8927 (m-80) cc_final: 0.8351 (m-80) REVERT: 7 37 ASN cc_start: 0.9222 (t0) cc_final: 0.8925 (t0) REVERT: 7 50 GLN cc_start: 0.8697 (tm130) cc_final: 0.8056 (tm130) REVERT: 7 54 PHE cc_start: 0.9235 (m-80) cc_final: 0.8674 (m-80) REVERT: 7 80 PHE cc_start: 0.8550 (m-10) cc_final: 0.8089 (m-80) REVERT: 8 14 LEU cc_start: 0.8376 (tm) cc_final: 0.8123 (tm) REVERT: 8 58 PHE cc_start: 0.9104 (m-80) cc_final: 0.8672 (m-80) REVERT: 8 69 PHE cc_start: 0.8945 (m-10) cc_final: 0.8419 (m-10) REVERT: 9 52 ARG cc_start: 0.8639 (tmm-80) cc_final: 0.8393 (ttt180) REVERT: 9 69 PHE cc_start: 0.9213 (m-10) cc_final: 0.8912 (m-80) REVERT: a 66 TRP cc_start: 0.8396 (m-90) cc_final: 0.8115 (m-90) REVERT: a 73 MET cc_start: 0.9562 (tpp) cc_final: 0.9126 (ttt) REVERT: a 74 ARG cc_start: 0.9349 (tmt-80) cc_final: 0.9102 (tpt90) REVERT: a 105 TRP cc_start: 0.7736 (m100) cc_final: 0.6940 (m100) REVERT: a 106 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8855 (mt) REVERT: a 181 LYS cc_start: 0.9371 (mttt) cc_final: 0.9077 (mmtp) REVERT: a 222 ASP cc_start: 0.8856 (m-30) cc_final: 0.8523 (m-30) REVERT: a 240 TYR cc_start: 0.9444 (m-10) cc_final: 0.9159 (m-10) REVERT: 1 52 ARG cc_start: 0.8324 (ptt-90) cc_final: 0.7715 (ptt90) REVERT: 1 78 PHE cc_start: 0.8147 (m-80) cc_final: 0.7928 (m-10) outliers start: 115 outliers final: 42 residues processed: 636 average time/residue: 0.5331 time to fit residues: 419.6413 Evaluate side-chains 598 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 537 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 295 GLN Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 2 residue 77 LEU Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 3 residue 82 THR Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 6 residue 55 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 57 PHE Chi-restraints excluded: chain 7 residue 77 LEU Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 59 ILE Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain 1 residue 9 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 353 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 296 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 408 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 403 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN G 37 GLN G 52 ASN G 131 GLN G 291 GLN H 44 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 ASN 2 37 ASN ** 7 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.058917 restraints weight = 90469.010| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.87 r_work: 0.2662 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 36230 Z= 0.193 Angle : 0.705 19.613 49213 Z= 0.348 Chirality : 0.046 0.432 5827 Planarity : 0.004 0.052 6370 Dihedral : 6.088 85.125 5333 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.08 % Allowed : 20.17 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.13), residues: 4807 helix: 1.58 (0.10), residues: 2632 sheet: -0.75 (0.22), residues: 540 loop : 0.43 (0.17), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG 7 52 TYR 0.034 0.002 TYR A 400 PHE 0.051 0.002 PHE 5 78 TRP 0.039 0.001 TRP a 212 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00452 (36230) covalent geometry : angle 0.70480 (49213) hydrogen bonds : bond 0.04356 ( 2293) hydrogen bonds : angle 4.79642 ( 6627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 573 time to evaluate : 1.327 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 45 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8399 (pp20) REVERT: A 182 CYS cc_start: 0.9400 (m) cc_final: 0.9188 (m) REVERT: A 225 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8647 (mp0) REVERT: A 251 TYR cc_start: 0.9414 (m-80) cc_final: 0.9144 (m-80) REVERT: A 335 ASN cc_start: 0.9536 (t0) cc_final: 0.9019 (t0) REVERT: A 443 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8600 (mt-10) REVERT: A 468 GLU cc_start: 0.8891 (pt0) cc_final: 0.8681 (pp20) REVERT: B 333 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8840 (mtmm) REVERT: B 356 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: B 369 ASN cc_start: 0.9075 (t0) cc_final: 0.8727 (t0) REVERT: B 413 LEU cc_start: 0.7446 (pt) cc_final: 0.7108 (pt) REVERT: B 448 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9189 (mp) REVERT: B 487 ARG cc_start: 0.8988 (mtm180) cc_final: 0.8704 (ttm110) REVERT: C 45 GLU cc_start: 0.8887 (pp20) cc_final: 0.8615 (pp20) REVERT: C 114 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9378 (mm) REVERT: C 331 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 335 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8668 (t160) REVERT: C 509 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8886 (mtmm) REVERT: D 67 MET cc_start: 0.9602 (mmm) cc_final: 0.9071 (mmm) REVERT: D 78 GLU cc_start: 0.9273 (tt0) cc_final: 0.8842 (tm-30) REVERT: D 185 SER cc_start: 0.9432 (OUTLIER) cc_final: 0.9037 (t) REVERT: D 203 GLU cc_start: 0.8800 (tp30) cc_final: 0.8477 (tp30) REVERT: D 287 MET cc_start: 0.9344 (tpp) cc_final: 0.9056 (tpp) REVERT: D 335 ARG cc_start: 0.9090 (mtp-110) cc_final: 0.8786 (tpp80) REVERT: D 383 GLN cc_start: 0.8952 (tp40) cc_final: 0.8630 (mm110) REVERT: E 45 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8817 (pp) REVERT: E 67 MET cc_start: 0.9341 (mmm) cc_final: 0.8879 (mmm) REVERT: E 123 LYS cc_start: 0.9626 (OUTLIER) cc_final: 0.9179 (mtpp) REVERT: E 158 LEU cc_start: 0.9220 (mp) cc_final: 0.8893 (mt) REVERT: E 222 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: E 273 MET cc_start: 0.9433 (mtp) cc_final: 0.9143 (mtt) REVERT: E 305 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8613 (tpp) REVERT: E 347 ASP cc_start: 0.9178 (t0) cc_final: 0.8588 (t0) REVERT: E 381 ASP cc_start: 0.9048 (m-30) cc_final: 0.8748 (m-30) REVERT: E 425 GLN cc_start: 0.8902 (mp10) cc_final: 0.8556 (mp10) REVERT: F 78 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8720 (tm-30) REVERT: F 254 ASP cc_start: 0.8748 (t0) cc_final: 0.8512 (t0) REVERT: F 255 ASN cc_start: 0.8565 (t0) cc_final: 0.8314 (t0) REVERT: F 289 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8210 (tp30) REVERT: F 347 ASP cc_start: 0.9454 (t0) cc_final: 0.9010 (t0) REVERT: F 422 PHE cc_start: 0.9087 (m-80) cc_final: 0.8699 (m-80) REVERT: F 444 LYS cc_start: 0.9358 (mtmt) cc_final: 0.9127 (mtmm) REVERT: G 19 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8752 (ttmm) REVERT: G 284 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8152 (tm-30) REVERT: H 7 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7576 (mm-30) REVERT: H 47 ASP cc_start: 0.9220 (m-30) cc_final: 0.8849 (p0) REVERT: H 48 ASP cc_start: 0.8982 (p0) cc_final: 0.8022 (t0) REVERT: H 82 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8084 (mm-30) REVERT: H 83 ASN cc_start: 0.9104 (t0) cc_final: 0.8869 (t0) REVERT: b 63 MET cc_start: 0.8674 (ttp) cc_final: 0.8169 (ppp) REVERT: b 66 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8909 (tmmt) REVERT: b 100 ARG cc_start: 0.8610 (mtp-110) cc_final: 0.8323 (mtp-110) REVERT: b 158 ARG cc_start: 0.9618 (mmm-85) cc_final: 0.8950 (tpp80) REVERT: d 53 ASP cc_start: 0.9681 (t0) cc_final: 0.9402 (m-30) REVERT: d 55 ASP cc_start: 0.9295 (t0) cc_final: 0.9026 (m-30) REVERT: d 186 LYS cc_start: 0.9555 (tptt) cc_final: 0.9332 (tmtm) REVERT: d 281 LYS cc_start: 0.9640 (tppt) cc_final: 0.9224 (tptp) REVERT: d 295 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.9118 (tp40) REVERT: d 366 GLU cc_start: 0.9474 (mm-30) cc_final: 0.8989 (tm-30) REVERT: 3 21 MET cc_start: 0.9024 (tmt) cc_final: 0.8326 (tmt) REVERT: 3 65 GLU cc_start: 0.9066 (tt0) cc_final: 0.8456 (tm-30) REVERT: 4 6 ASN cc_start: 0.8502 (p0) cc_final: 0.7884 (t0) REVERT: 4 58 PHE cc_start: 0.8850 (m-10) cc_final: 0.8589 (m-10) REVERT: 4 75 MET cc_start: 0.9419 (tmm) cc_final: 0.9063 (tmm) REVERT: 5 14 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6045 (tm) REVERT: 5 75 MET cc_start: 0.8592 (ttp) cc_final: 0.8280 (ttp) REVERT: 6 6 ASN cc_start: 0.8865 (m-40) cc_final: 0.8565 (p0) REVERT: 6 37 ASN cc_start: 0.9302 (t0) cc_final: 0.8779 (m-40) REVERT: 6 54 PHE cc_start: 0.8909 (m-80) cc_final: 0.8346 (m-80) REVERT: 7 37 ASN cc_start: 0.9166 (t0) cc_final: 0.8384 (m110) REVERT: 7 50 GLN cc_start: 0.8679 (tm130) cc_final: 0.7969 (tm130) REVERT: 7 54 PHE cc_start: 0.9313 (m-80) cc_final: 0.8758 (m-80) REVERT: 7 80 PHE cc_start: 0.8481 (m-10) cc_final: 0.8026 (m-80) REVERT: 8 58 PHE cc_start: 0.9115 (m-80) cc_final: 0.8685 (m-80) REVERT: 8 65 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8389 (tp30) REVERT: 8 75 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8306 (mmm) REVERT: 9 69 PHE cc_start: 0.9242 (m-10) cc_final: 0.8955 (m-80) REVERT: 9 78 PHE cc_start: 0.7638 (t80) cc_final: 0.7343 (t80) REVERT: a 66 TRP cc_start: 0.8422 (m-90) cc_final: 0.8049 (m-90) REVERT: a 73 MET cc_start: 0.9548 (tpp) cc_final: 0.9104 (ttt) REVERT: a 74 ARG cc_start: 0.9314 (tmt-80) cc_final: 0.9104 (tpt90) REVERT: a 105 TRP cc_start: 0.7942 (m100) cc_final: 0.7029 (m100) REVERT: a 106 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8747 (mt) REVERT: a 124 TYR cc_start: 0.6495 (t80) cc_final: 0.6154 (t80) REVERT: a 181 LYS cc_start: 0.9374 (mttt) cc_final: 0.9108 (mmtp) REVERT: a 222 ASP cc_start: 0.8928 (m-30) cc_final: 0.8572 (m-30) REVERT: a 227 LEU cc_start: 0.9307 (pp) cc_final: 0.9063 (pt) REVERT: a 240 TYR cc_start: 0.9440 (m-10) cc_final: 0.9074 (m-10) REVERT: a 245 MET cc_start: 0.9118 (mtp) cc_final: 0.8808 (mtp) REVERT: 1 52 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8051 (ptt90) outliers start: 107 outliers final: 42 residues processed: 628 average time/residue: 0.5274 time to fit residues: 411.2331 Evaluate side-chains 607 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 545 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 295 GLN Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 2 residue 77 LEU Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 82 THR Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 6 residue 55 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 57 PHE Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 59 ILE Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain 1 residue 9 ILE Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 52 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 271 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 316 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 390 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 289 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 443 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN E 117 HIS G 37 GLN G 52 ASN G 131 GLN G 291 GLN H 44 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 ASN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 37 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.059398 restraints weight = 90115.934| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.84 r_work: 0.2632 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 36230 Z= 0.262 Angle : 0.749 18.309 49213 Z= 0.370 Chirality : 0.047 0.468 5827 Planarity : 0.004 0.052 6370 Dihedral : 6.093 88.896 5331 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.91 % Allowed : 21.26 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.13), residues: 4807 helix: 1.57 (0.10), residues: 2636 sheet: -0.77 (0.22), residues: 546 loop : 0.44 (0.17), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 4 52 TYR 0.039 0.002 TYR A 400 PHE 0.055 0.002 PHE 5 78 TRP 0.043 0.002 TRP a 212 HIS 0.004 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00608 (36230) covalent geometry : angle 0.74884 (49213) hydrogen bonds : bond 0.04496 ( 2293) hydrogen bonds : angle 4.82333 ( 6627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 548 time to evaluate : 1.218 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 45 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8381 (pp20) REVERT: A 182 CYS cc_start: 0.9396 (m) cc_final: 0.9180 (m) REVERT: A 225 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8678 (mp0) REVERT: A 251 TYR cc_start: 0.9450 (m-80) cc_final: 0.9149 (m-80) REVERT: A 335 ASN cc_start: 0.9419 (t0) cc_final: 0.9090 (t0) REVERT: A 443 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8649 (mt-10) REVERT: B 333 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8837 (mtmm) REVERT: B 356 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: B 369 ASN cc_start: 0.9043 (t0) cc_final: 0.8630 (t0) REVERT: B 413 LEU cc_start: 0.7447 (pt) cc_final: 0.7100 (pt) REVERT: B 448 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9192 (mp) REVERT: B 487 ARG cc_start: 0.8983 (mtm180) cc_final: 0.8718 (ttm110) REVERT: C 114 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9437 (mm) REVERT: C 331 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7801 (tm-30) REVERT: C 335 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8648 (t160) REVERT: C 509 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8987 (mtmm) REVERT: D 67 MET cc_start: 0.9594 (mmm) cc_final: 0.9060 (mmm) REVERT: D 78 GLU cc_start: 0.9279 (tt0) cc_final: 0.8858 (tm-30) REVERT: D 185 SER cc_start: 0.9454 (OUTLIER) cc_final: 0.9093 (t) REVERT: D 203 GLU cc_start: 0.8821 (tp30) cc_final: 0.8428 (tp30) REVERT: D 287 MET cc_start: 0.9356 (tpp) cc_final: 0.9009 (tpp) REVERT: D 335 ARG cc_start: 0.9121 (mtp-110) cc_final: 0.8824 (tpp80) REVERT: D 383 GLN cc_start: 0.8993 (tp40) cc_final: 0.8671 (mm110) REVERT: E 45 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8825 (pp) REVERT: E 67 MET cc_start: 0.9355 (mmm) cc_final: 0.8815 (mmm) REVERT: E 123 LYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9220 (mtpp) REVERT: E 158 LEU cc_start: 0.9233 (mp) cc_final: 0.8899 (mt) REVERT: E 222 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: E 273 MET cc_start: 0.9424 (mtp) cc_final: 0.9166 (mtm) REVERT: E 305 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8615 (tpp) REVERT: E 347 ASP cc_start: 0.9174 (t0) cc_final: 0.8613 (t0) REVERT: E 381 ASP cc_start: 0.9053 (m-30) cc_final: 0.8769 (m-30) REVERT: F 78 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8708 (tm-30) REVERT: F 254 ASP cc_start: 0.8757 (t0) cc_final: 0.8505 (t0) REVERT: F 255 ASN cc_start: 0.8641 (t0) cc_final: 0.8381 (t0) REVERT: F 289 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8223 (tp30) REVERT: F 347 ASP cc_start: 0.9444 (t0) cc_final: 0.8982 (t0) REVERT: F 422 PHE cc_start: 0.9115 (m-80) cc_final: 0.8749 (m-80) REVERT: F 444 LYS cc_start: 0.9363 (mtmt) cc_final: 0.9159 (mtmm) REVERT: G 19 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8764 (ttmm) REVERT: G 284 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8102 (tm-30) REVERT: H 47 ASP cc_start: 0.9254 (m-30) cc_final: 0.8886 (p0) REVERT: H 48 ASP cc_start: 0.8986 (p0) cc_final: 0.8025 (t0) REVERT: H 82 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8095 (mm-30) REVERT: H 83 ASN cc_start: 0.9131 (t0) cc_final: 0.8888 (t0) REVERT: b 63 MET cc_start: 0.8652 (ttp) cc_final: 0.8157 (ppp) REVERT: b 66 LYS cc_start: 0.9279 (mmtt) cc_final: 0.8922 (tmmt) REVERT: b 100 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8400 (mtp-110) REVERT: b 158 ARG cc_start: 0.9588 (mmm-85) cc_final: 0.8830 (tpp80) REVERT: d 53 ASP cc_start: 0.9686 (t0) cc_final: 0.9429 (m-30) REVERT: d 55 ASP cc_start: 0.9313 (t0) cc_final: 0.9025 (m-30) REVERT: d 186 LYS cc_start: 0.9530 (tptt) cc_final: 0.9312 (tmtm) REVERT: d 281 LYS cc_start: 0.9642 (tppt) cc_final: 0.9294 (tptp) REVERT: d 295 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9125 (tp40) REVERT: d 366 GLU cc_start: 0.9478 (mm-30) cc_final: 0.8998 (tm-30) REVERT: 2 65 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: 2 71 ASN cc_start: 0.7795 (t0) cc_final: 0.7079 (t0) REVERT: 3 20 ILE cc_start: 0.8662 (mm) cc_final: 0.8383 (mm) REVERT: 3 65 GLU cc_start: 0.9070 (tt0) cc_final: 0.8456 (tm-30) REVERT: 3 69 PHE cc_start: 0.8418 (m-10) cc_final: 0.7970 (m-10) REVERT: 4 6 ASN cc_start: 0.8517 (p0) cc_final: 0.7910 (t0) REVERT: 4 54 PHE cc_start: 0.7880 (p90) cc_final: 0.7610 (p90) REVERT: 4 58 PHE cc_start: 0.8835 (m-10) cc_final: 0.8610 (m-10) REVERT: 4 75 MET cc_start: 0.9501 (tmm) cc_final: 0.9296 (tpt) REVERT: 4 78 PHE cc_start: 0.4617 (t80) cc_final: 0.4225 (t80) REVERT: 5 14 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6085 (tm) REVERT: 5 57 PHE cc_start: 0.9473 (t80) cc_final: 0.9073 (t80) REVERT: 5 75 MET cc_start: 0.8798 (ttp) cc_final: 0.8504 (ttp) REVERT: 6 6 ASN cc_start: 0.8996 (m-40) cc_final: 0.8699 (p0) REVERT: 6 37 ASN cc_start: 0.9305 (t0) cc_final: 0.8782 (m110) REVERT: 6 52 ARG cc_start: 0.8944 (ptp90) cc_final: 0.8398 (ptt90) REVERT: 6 54 PHE cc_start: 0.9009 (m-80) cc_final: 0.8443 (m-80) REVERT: 7 37 ASN cc_start: 0.9130 (t0) cc_final: 0.8863 (t0) REVERT: 7 50 GLN cc_start: 0.8634 (tm130) cc_final: 0.7816 (tm130) REVERT: 7 54 PHE cc_start: 0.9347 (m-80) cc_final: 0.8849 (m-80) REVERT: 7 75 MET cc_start: 0.8099 (tmm) cc_final: 0.7709 (tmm) REVERT: 7 79 VAL cc_start: 0.8491 (p) cc_final: 0.8241 (p) REVERT: 7 80 PHE cc_start: 0.8338 (m-10) cc_final: 0.7894 (m-80) REVERT: 8 21 MET cc_start: 0.8420 (tpp) cc_final: 0.7916 (tpt) REVERT: 8 58 PHE cc_start: 0.9138 (m-80) cc_final: 0.8687 (m-80) REVERT: 8 75 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8548 (mmt) REVERT: 9 69 PHE cc_start: 0.9211 (m-10) cc_final: 0.8929 (m-80) REVERT: a 66 TRP cc_start: 0.8640 (m-90) cc_final: 0.8262 (m-90) REVERT: a 72 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: a 73 MET cc_start: 0.9553 (tpp) cc_final: 0.9112 (ttp) REVERT: a 105 TRP cc_start: 0.8063 (m100) cc_final: 0.7278 (m100) REVERT: a 106 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8818 (mt) REVERT: a 122 GLU cc_start: 0.7859 (tp30) cc_final: 0.7648 (tp30) REVERT: a 181 LYS cc_start: 0.9390 (mttt) cc_final: 0.9148 (mmtp) REVERT: a 222 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8647 (m-30) REVERT: a 240 TYR cc_start: 0.9436 (m-10) cc_final: 0.9126 (m-10) REVERT: a 245 MET cc_start: 0.9158 (mtp) cc_final: 0.8863 (mtp) REVERT: 1 52 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8284 (ppt-90) outliers start: 101 outliers final: 41 residues processed: 599 average time/residue: 0.5330 time to fit residues: 394.4448 Evaluate side-chains 598 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 534 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 295 GLN Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 2 residue 77 LEU Chi-restraints excluded: chain 3 residue 19 LEU Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 30 ILE Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 6 residue 55 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 19 LEU Chi-restraints excluded: chain 7 residue 59 ILE Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 52 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 439 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 320 optimal weight: 1.9990 chunk 460 optimal weight: 30.0000 chunk 4 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN F 400 GLN G 52 ASN G 131 GLN H 85 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 ASN 2 37 ASN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 ASN a 174 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.061149 restraints weight = 90289.752| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.78 r_work: 0.2657 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36230 Z= 0.186 Angle : 0.750 17.979 49213 Z= 0.366 Chirality : 0.046 0.448 5827 Planarity : 0.004 0.067 6370 Dihedral : 6.022 86.421 5331 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.42 % Allowed : 22.27 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.13), residues: 4807 helix: 1.59 (0.10), residues: 2631 sheet: -0.71 (0.23), residues: 521 loop : 0.44 (0.17), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 6 45 TYR 0.039 0.002 TYR A 400 PHE 0.070 0.002 PHE 7 74 TRP 0.048 0.002 TRP a 212 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00431 (36230) covalent geometry : angle 0.74969 (49213) hydrogen bonds : bond 0.04389 ( 2293) hydrogen bonds : angle 4.80523 ( 6627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 561 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8334 (pp20) REVERT: A 182 CYS cc_start: 0.9408 (m) cc_final: 0.9187 (m) REVERT: A 225 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8634 (mp0) REVERT: A 251 TYR cc_start: 0.9389 (m-80) cc_final: 0.9075 (m-80) REVERT: A 335 ASN cc_start: 0.9492 (t0) cc_final: 0.9073 (t0) REVERT: A 443 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8509 (mt-10) REVERT: B 356 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: B 369 ASN cc_start: 0.9056 (t0) cc_final: 0.8641 (t0) REVERT: B 448 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9128 (mp) REVERT: B 487 ARG cc_start: 0.8969 (mtm180) cc_final: 0.8644 (ttm110) REVERT: B 488 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8865 (mm-30) REVERT: C 45 GLU cc_start: 0.8831 (pp20) cc_final: 0.8575 (pp20) REVERT: C 114 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9315 (mm) REVERT: C 331 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 335 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8772 (t0) REVERT: C 509 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8980 (mtmm) REVERT: D 67 MET cc_start: 0.9580 (mmm) cc_final: 0.9030 (mmm) REVERT: D 78 GLU cc_start: 0.9273 (tt0) cc_final: 0.8816 (tm-30) REVERT: D 185 SER cc_start: 0.9446 (OUTLIER) cc_final: 0.9046 (t) REVERT: D 203 GLU cc_start: 0.8781 (tp30) cc_final: 0.8378 (tp30) REVERT: D 287 MET cc_start: 0.9291 (tpp) cc_final: 0.9000 (tpp) REVERT: D 335 ARG cc_start: 0.9091 (mtp-110) cc_final: 0.8789 (tpp80) REVERT: D 383 GLN cc_start: 0.8964 (tp40) cc_final: 0.8625 (mm110) REVERT: E 45 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8758 (pp) REVERT: E 67 MET cc_start: 0.9325 (mmm) cc_final: 0.8832 (mmm) REVERT: E 123 LYS cc_start: 0.9619 (OUTLIER) cc_final: 0.9195 (mtpp) REVERT: E 158 LEU cc_start: 0.9132 (mp) cc_final: 0.8800 (mt) REVERT: E 222 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: E 273 MET cc_start: 0.9420 (mtp) cc_final: 0.9153 (mtt) REVERT: E 305 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8580 (tpp) REVERT: E 347 ASP cc_start: 0.9111 (t0) cc_final: 0.8535 (t0) REVERT: E 425 GLN cc_start: 0.8892 (mp10) cc_final: 0.8542 (mp10) REVERT: F 78 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8705 (tm-30) REVERT: F 254 ASP cc_start: 0.8750 (t0) cc_final: 0.8474 (t0) REVERT: F 255 ASN cc_start: 0.8445 (t0) cc_final: 0.8188 (t0) REVERT: F 289 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8219 (tp30) REVERT: F 330 THR cc_start: 0.9190 (m) cc_final: 0.8745 (t) REVERT: F 347 ASP cc_start: 0.9409 (t0) cc_final: 0.8966 (t0) REVERT: F 422 PHE cc_start: 0.9038 (m-80) cc_final: 0.8717 (m-80) REVERT: G 19 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8703 (ttmm) REVERT: G 284 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8076 (tm-30) REVERT: H 47 ASP cc_start: 0.9255 (m-30) cc_final: 0.8892 (p0) REVERT: H 48 ASP cc_start: 0.8967 (p0) cc_final: 0.8043 (t0) REVERT: H 54 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8254 (mm-30) REVERT: H 82 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8091 (mm-30) REVERT: H 83 ASN cc_start: 0.9124 (t0) cc_final: 0.8886 (t0) REVERT: b 63 MET cc_start: 0.8634 (ttp) cc_final: 0.8154 (ppp) REVERT: b 66 LYS cc_start: 0.9238 (mmtt) cc_final: 0.8881 (tmmt) REVERT: b 158 ARG cc_start: 0.9564 (mmm-85) cc_final: 0.8852 (tpp80) REVERT: d 55 ASP cc_start: 0.9338 (t0) cc_final: 0.9049 (m-30) REVERT: d 186 LYS cc_start: 0.9545 (tptt) cc_final: 0.9322 (tmtm) REVERT: d 221 LYS cc_start: 0.8678 (pptt) cc_final: 0.8432 (pptt) REVERT: d 281 LYS cc_start: 0.9641 (tppt) cc_final: 0.9271 (tptp) REVERT: d 295 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9123 (tp40) REVERT: d 366 GLU cc_start: 0.9483 (mm-30) cc_final: 0.8996 (tm-30) REVERT: 2 21 MET cc_start: 0.7691 (tpp) cc_final: 0.7223 (mmt) REVERT: 2 65 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8601 (mp0) REVERT: 2 71 ASN cc_start: 0.8018 (t0) cc_final: 0.7486 (t0) REVERT: 3 20 ILE cc_start: 0.8565 (mm) cc_final: 0.8234 (mm) REVERT: 3 65 GLU cc_start: 0.9016 (tt0) cc_final: 0.8367 (tm-30) REVERT: 3 69 PHE cc_start: 0.8337 (m-10) cc_final: 0.7954 (m-10) REVERT: 3 75 MET cc_start: 0.8864 (tmm) cc_final: 0.8435 (ttm) REVERT: 4 6 ASN cc_start: 0.8506 (p0) cc_final: 0.7919 (t0) REVERT: 4 54 PHE cc_start: 0.7837 (p90) cc_final: 0.7565 (p90) REVERT: 4 58 PHE cc_start: 0.8805 (m-10) cc_final: 0.8596 (m-80) REVERT: 4 75 MET cc_start: 0.9382 (tmm) cc_final: 0.9177 (tpt) REVERT: 4 78 PHE cc_start: 0.5245 (t80) cc_final: 0.3941 (t80) REVERT: 5 14 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6078 (tm) REVERT: 5 54 PHE cc_start: 0.8314 (m-10) cc_final: 0.8072 (m-10) REVERT: 5 57 PHE cc_start: 0.9435 (t80) cc_final: 0.9076 (t80) REVERT: 5 75 MET cc_start: 0.8866 (ttp) cc_final: 0.8610 (ttp) REVERT: 6 6 ASN cc_start: 0.8986 (m-40) cc_final: 0.8783 (p0) REVERT: 6 37 ASN cc_start: 0.9219 (t0) cc_final: 0.8702 (m110) REVERT: 6 52 ARG cc_start: 0.8934 (ptp90) cc_final: 0.8609 (ptt-90) REVERT: 6 54 PHE cc_start: 0.9040 (m-80) cc_final: 0.8522 (m-80) REVERT: 7 37 ASN cc_start: 0.9032 (t0) cc_final: 0.8769 (t0) REVERT: 7 50 GLN cc_start: 0.8631 (tm130) cc_final: 0.7871 (tm130) REVERT: 7 54 PHE cc_start: 0.9402 (m-80) cc_final: 0.8998 (m-80) REVERT: 7 78 PHE cc_start: 0.8490 (t80) cc_final: 0.8154 (t80) REVERT: 7 79 VAL cc_start: 0.8468 (p) cc_final: 0.8257 (p) REVERT: 7 80 PHE cc_start: 0.8219 (m-10) cc_final: 0.7752 (m-80) REVERT: 8 21 MET cc_start: 0.8312 (tpp) cc_final: 0.7742 (tpt) REVERT: 8 58 PHE cc_start: 0.9140 (m-80) cc_final: 0.8695 (m-80) REVERT: 8 65 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8301 (tp30) REVERT: 8 75 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8358 (mmt) REVERT: 9 52 ARG cc_start: 0.8985 (ttt180) cc_final: 0.8741 (ptm160) REVERT: a 66 TRP cc_start: 0.8713 (m-90) cc_final: 0.8242 (m-90) REVERT: a 72 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: a 73 MET cc_start: 0.9557 (tpp) cc_final: 0.9086 (ttp) REVERT: a 105 TRP cc_start: 0.7944 (m100) cc_final: 0.7172 (m100) REVERT: a 146 HIS cc_start: 0.8620 (m-70) cc_final: 0.7906 (m-70) REVERT: a 151 TRP cc_start: 0.9323 (t-100) cc_final: 0.8910 (t60) REVERT: a 188 ARG cc_start: 0.9229 (ttm110) cc_final: 0.8609 (ptp-110) REVERT: a 222 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8643 (m-30) REVERT: a 236 LEU cc_start: 0.9790 (mt) cc_final: 0.9344 (tm) REVERT: a 245 MET cc_start: 0.9122 (mtp) cc_final: 0.8891 (mtp) REVERT: 1 45 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7482 (mmm-85) REVERT: 1 52 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7900 (ptt90) outliers start: 84 outliers final: 37 residues processed: 598 average time/residue: 0.5231 time to fit residues: 388.1707 Evaluate side-chains 594 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 535 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 295 GLN Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 2 residue 77 LEU Chi-restraints excluded: chain 3 residue 19 LEU Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 6 residue 55 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 19 LEU Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain 1 residue 52 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 182 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 368 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 175 ASN G 52 ASN G 131 GLN H 44 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 ASN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 37 ASN ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.058888 restraints weight = 91179.133| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.79 r_work: 0.2619 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 36230 Z= 0.281 Angle : 0.802 16.611 49213 Z= 0.394 Chirality : 0.048 0.435 5827 Planarity : 0.005 0.059 6370 Dihedral : 6.091 89.472 5331 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.30 % Allowed : 23.02 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.13), residues: 4807 helix: 1.53 (0.10), residues: 2637 sheet: -0.76 (0.22), residues: 540 loop : 0.44 (0.17), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a 74 TYR 0.047 0.002 TYR 7 68 PHE 0.064 0.002 PHE 7 74 TRP 0.046 0.002 TRP a 212 HIS 0.005 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00646 (36230) covalent geometry : angle 0.80170 (49213) hydrogen bonds : bond 0.04554 ( 2293) hydrogen bonds : angle 4.87567 ( 6627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 534 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8326 (pp20) REVERT: A 182 CYS cc_start: 0.9427 (m) cc_final: 0.9211 (m) REVERT: A 225 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8655 (mp0) REVERT: A 251 TYR cc_start: 0.9443 (m-80) cc_final: 0.9147 (m-80) REVERT: A 335 ASN cc_start: 0.9490 (t0) cc_final: 0.9073 (t0) REVERT: A 443 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: B 356 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: B 369 ASN cc_start: 0.9054 (t0) cc_final: 0.8581 (t0) REVERT: B 487 ARG cc_start: 0.8988 (mtm180) cc_final: 0.8357 (mtm110) REVERT: B 488 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8789 (mm-30) REVERT: C 45 GLU cc_start: 0.8891 (pp20) cc_final: 0.8652 (pp20) REVERT: C 114 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9425 (mm) REVERT: C 331 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7829 (tm-30) REVERT: C 335 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.7917 (t0) REVERT: C 356 GLU cc_start: 0.8562 (tt0) cc_final: 0.8206 (tp30) REVERT: C 509 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8971 (mtmm) REVERT: D 67 MET cc_start: 0.9591 (mmm) cc_final: 0.9021 (mmm) REVERT: D 78 GLU cc_start: 0.9286 (tt0) cc_final: 0.8832 (tm-30) REVERT: D 185 SER cc_start: 0.9475 (OUTLIER) cc_final: 0.9078 (t) REVERT: D 203 GLU cc_start: 0.8815 (tp30) cc_final: 0.8425 (tp30) REVERT: D 287 MET cc_start: 0.9327 (tpp) cc_final: 0.8988 (tpp) REVERT: D 335 ARG cc_start: 0.9127 (mtp-110) cc_final: 0.8826 (tpp80) REVERT: D 383 GLN cc_start: 0.8966 (tp40) cc_final: 0.8636 (mm110) REVERT: E 45 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8829 (pp) REVERT: E 67 MET cc_start: 0.9337 (mmm) cc_final: 0.8803 (mmm) REVERT: E 123 LYS cc_start: 0.9613 (OUTLIER) cc_final: 0.9205 (mtpp) REVERT: E 158 LEU cc_start: 0.9194 (mp) cc_final: 0.8852 (mt) REVERT: E 222 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: E 239 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8421 (mt-10) REVERT: E 273 MET cc_start: 0.9439 (mtp) cc_final: 0.9155 (mtt) REVERT: E 305 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8567 (tpp) REVERT: E 347 ASP cc_start: 0.9126 (t0) cc_final: 0.8549 (t0) REVERT: E 381 ASP cc_start: 0.9019 (m-30) cc_final: 0.8728 (m-30) REVERT: F 78 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: F 254 ASP cc_start: 0.8766 (t0) cc_final: 0.8510 (t0) REVERT: F 255 ASN cc_start: 0.8556 (t0) cc_final: 0.8281 (t0) REVERT: F 289 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8250 (tp30) REVERT: F 347 ASP cc_start: 0.9413 (t0) cc_final: 0.8939 (t0) REVERT: F 422 PHE cc_start: 0.9076 (m-80) cc_final: 0.8737 (m-80) REVERT: G 19 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8725 (ttmm) REVERT: G 263 MET cc_start: 0.9020 (mmp) cc_final: 0.8816 (mmp) REVERT: G 284 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8166 (tm-30) REVERT: H 7 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7871 (mp0) REVERT: H 47 ASP cc_start: 0.9264 (m-30) cc_final: 0.8874 (p0) REVERT: H 48 ASP cc_start: 0.8975 (p0) cc_final: 0.8071 (t0) REVERT: H 54 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8247 (mm-30) REVERT: H 82 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8084 (mm-30) REVERT: H 83 ASN cc_start: 0.9083 (t0) cc_final: 0.8843 (t0) REVERT: b 63 MET cc_start: 0.8684 (ttp) cc_final: 0.8210 (ppp) REVERT: b 66 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8912 (tmmt) REVERT: b 158 ARG cc_start: 0.9585 (mmm-85) cc_final: 0.8774 (tpp80) REVERT: d 55 ASP cc_start: 0.9275 (t0) cc_final: 0.9004 (m-30) REVERT: d 186 LYS cc_start: 0.9541 (tptt) cc_final: 0.9325 (tmtm) REVERT: d 221 LYS cc_start: 0.8669 (pptt) cc_final: 0.8409 (pptt) REVERT: d 281 LYS cc_start: 0.9634 (tppt) cc_final: 0.9257 (tptp) REVERT: d 295 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.9163 (tp40) REVERT: d 366 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9051 (tm-30) REVERT: 2 21 MET cc_start: 0.7638 (tpp) cc_final: 0.7346 (mmt) REVERT: 2 65 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: 2 71 ASN cc_start: 0.7877 (t0) cc_final: 0.7472 (t0) REVERT: 2 75 MET cc_start: 0.7181 (ppp) cc_final: 0.6827 (ppp) REVERT: 3 20 ILE cc_start: 0.8552 (mm) cc_final: 0.8260 (mm) REVERT: 3 65 GLU cc_start: 0.9006 (tt0) cc_final: 0.8324 (tm-30) REVERT: 3 71 ASN cc_start: 0.8406 (m-40) cc_final: 0.7755 (m110) REVERT: 4 6 ASN cc_start: 0.8533 (p0) cc_final: 0.7937 (t0) REVERT: 4 54 PHE cc_start: 0.7768 (p90) cc_final: 0.7486 (p90) REVERT: 4 58 PHE cc_start: 0.8833 (m-10) cc_final: 0.8621 (m-80) REVERT: 4 75 MET cc_start: 0.9383 (tmm) cc_final: 0.9158 (tpt) REVERT: 4 78 PHE cc_start: 0.5028 (t80) cc_final: 0.4118 (t80) REVERT: 5 14 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6192 (tm) REVERT: 5 50 GLN cc_start: 0.8489 (tm130) cc_final: 0.8246 (tm-30) REVERT: 5 57 PHE cc_start: 0.9451 (t80) cc_final: 0.9124 (t80) REVERT: 6 6 ASN cc_start: 0.8932 (m-40) cc_final: 0.8726 (p0) REVERT: 6 52 ARG cc_start: 0.8861 (ptp90) cc_final: 0.8320 (ptt90) REVERT: 6 54 PHE cc_start: 0.9026 (m-80) cc_final: 0.8486 (m-80) REVERT: 7 50 GLN cc_start: 0.8663 (tm130) cc_final: 0.7767 (tm130) REVERT: 7 54 PHE cc_start: 0.9430 (m-80) cc_final: 0.8979 (m-80) REVERT: 7 75 MET cc_start: 0.7648 (tmm) cc_final: 0.7440 (ppp) REVERT: 7 78 PHE cc_start: 0.8417 (t80) cc_final: 0.8122 (t80) REVERT: 7 80 PHE cc_start: 0.8151 (m-10) cc_final: 0.7659 (m-80) REVERT: 8 21 MET cc_start: 0.8189 (tpp) cc_final: 0.7487 (tpt) REVERT: 8 53 LEU cc_start: 0.9482 (mm) cc_final: 0.9192 (pp) REVERT: 8 58 PHE cc_start: 0.9134 (m-80) cc_final: 0.8723 (m-80) REVERT: 8 65 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8327 (tp30) REVERT: 8 75 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8460 (mmt) REVERT: 9 74 PHE cc_start: 0.7784 (t80) cc_final: 0.7555 (t80) REVERT: a 66 TRP cc_start: 0.8799 (m-90) cc_final: 0.8330 (m-90) REVERT: a 72 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: a 73 MET cc_start: 0.9547 (tpp) cc_final: 0.9041 (tpp) REVERT: a 105 TRP cc_start: 0.7997 (m100) cc_final: 0.7205 (m100) REVERT: a 146 HIS cc_start: 0.8533 (m-70) cc_final: 0.7740 (m-70) REVERT: a 151 TRP cc_start: 0.9274 (t-100) cc_final: 0.8866 (t60) REVERT: a 222 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: a 236 LEU cc_start: 0.9806 (mt) cc_final: 0.9372 (tm) REVERT: a 245 MET cc_start: 0.9156 (mtp) cc_final: 0.8947 (mtp) REVERT: 1 45 ARG cc_start: 0.7738 (mmt90) cc_final: 0.7450 (mmm-85) REVERT: 1 78 PHE cc_start: 0.8389 (m-80) cc_final: 0.8144 (m-80) outliers start: 80 outliers final: 41 residues processed: 574 average time/residue: 0.5338 time to fit residues: 379.3052 Evaluate side-chains 576 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 515 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 295 GLN Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 2 residue 77 LEU Chi-restraints excluded: chain 3 residue 19 LEU Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 6 residue 55 THR Chi-restraints excluded: chain 6 residue 85 LEU Chi-restraints excluded: chain 7 residue 19 LEU Chi-restraints excluded: chain 7 residue 59 ILE Chi-restraints excluded: chain 8 residue 37 ASN Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 8 residue 78 PHE Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 178 GLU Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain 1 residue 52 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 422 optimal weight: 0.9990 chunk 350 optimal weight: 10.0000 chunk 477 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 478 optimal weight: 20.0000 chunk 238 optimal weight: 0.9980 chunk 479 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 361 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN G 52 ASN G 131 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 ASN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061016 restraints weight = 89809.857| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.82 r_work: 0.2667 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 36230 Z= 0.170 Angle : 0.779 18.447 49213 Z= 0.380 Chirality : 0.047 0.402 5827 Planarity : 0.005 0.062 6370 Dihedral : 6.028 84.905 5331 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.30 % Allowed : 23.34 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.13), residues: 4807 helix: 1.54 (0.10), residues: 2629 sheet: -0.73 (0.23), residues: 521 loop : 0.49 (0.17), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG a 188 TYR 0.039 0.002 TYR A 400 PHE 0.062 0.002 PHE 7 74 TRP 0.046 0.002 TRP a 212 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00396 (36230) covalent geometry : angle 0.77922 (49213) hydrogen bonds : bond 0.04412 ( 2293) hydrogen bonds : angle 4.84756 ( 6627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12168.21 seconds wall clock time: 207 minutes 30.54 seconds (12450.54 seconds total)