Starting phenix.real_space_refine on Fri Mar 6 22:53:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n2z_9334/03_2026/6n2z_9334.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n2z_9334/03_2026/6n2z_9334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n2z_9334/03_2026/6n2z_9334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n2z_9334/03_2026/6n2z_9334.map" model { file = "/net/cci-nas-00/data/ceres_data/6n2z_9334/03_2026/6n2z_9334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n2z_9334/03_2026/6n2z_9334.cif" } resolution = 3.0 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= 0.009 sd= 0.211 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 12 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 22297 2.51 5 N 6105 2.21 5 O 6537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35051 Number of models: 1 Model: "" Number of chains: 28 Chain: "b2" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 771 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 1, 'TRANS': 132} Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU:plan': 22, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 186 Chain: "b2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "b1" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 890 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 1, 'TRANS': 155} Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 14, 'GLU:plan': 27, 'ASN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 238 Chain: "a" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1486 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "c7" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c8" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c9" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c0" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c1" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c2" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c3" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c4" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c6" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "B" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3806 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 475} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3725 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 470} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3833 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3618 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} 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: "F" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3578 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3614 Classifications: {'peptide': 471} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2205 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 927 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "I" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1314 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 56 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: "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: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.26, per 1000 atoms: 0.24 Number of scatterers: 35051 At special positions: 0 Unit cell: (117.66, 135.68, 227.9, 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 96 16.00 P 12 15.00 Mg 4 11.99 O 6537 8.00 N 6105 7.00 C 22297 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8580 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 25 sheets defined 58.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'b2' and resid 10 through 29 Processing helix chain 'b2' and resid 29 through 140 removed outlier: 3.724A pdb=" N ILEb2 44 " --> pdb=" O ARGb2 40 " (cutoff:3.500A) Processing helix chain 'b2' and resid 601 through 616 Processing helix chain 'b1' and resid 9 through 143 removed outlier: 3.610A pdb=" N TYRb1 13 " --> pdb=" O GLYb1 9 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRPb1 30 " --> pdb=" O ARGb1 26 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNb1 31 " --> pdb=" O LYSb1 27 " (cutoff:3.500A) Proline residue: b1 32 - end of helix Processing helix chain 'b1' and resid 145 through 163 removed outlier: 3.722A pdb=" N ARGb1 150 " --> pdb=" O GLUb1 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 38 removed outlier: 3.582A pdb=" N MET a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 67 Processing helix chain 'a' and resid 68 through 73 Processing helix chain 'a' and resid 75 through 92 removed outlier: 3.745A pdb=" N THR a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 130 Processing helix chain 'a' and resid 153 through 191 removed outlier: 4.630A pdb=" N GLY a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR a 191 " --> pdb=" O LEU a 187 " (cutoff:3.500A) Processing helix chain 'a' and resid 199 through 234 removed outlier: 4.262A pdb=" N MET a 203 " --> pdb=" O ALA a 199 " (cutoff:3.500A) Processing helix chain 'c7' and resid 3 through 37 Processing helix chain 'c7' and resid 40 through 72 removed outlier: 4.002A pdb=" N THRc7 47 " --> pdb=" O VALc7 43 " (cutoff:3.500A) Proline residue: c7 59 - end of helix removed outlier: 3.924A pdb=" N PHEc7 67 " --> pdb=" O VALc7 63 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILEc7 68 " --> pdb=" O VALc7 64 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARGc7 72 " --> pdb=" O ILEc7 68 " (cutoff:3.500A) Processing helix chain 'c8' and resid 3 through 37 Processing helix chain 'c8' and resid 40 through 72 removed outlier: 4.525A pdb=" N LEUc8 58 " --> pdb=" O LEUc8 54 " (cutoff:3.500A) Proline residue: c8 59 - end of helix Processing helix chain 'c9' and resid 3 through 37 Processing helix chain 'c9' and resid 40 through 56 Processing helix chain 'c9' and resid 56 through 72 Processing helix chain 'c0' and resid 3 through 37 Processing helix chain 'c0' and resid 40 through 71 Proline residue: c0 59 - end of helix Processing helix chain 'c1' and resid 3 through 37 Processing helix chain 'c1' and resid 40 through 56 Processing helix chain 'c1' and resid 56 through 72 removed outlier: 4.032A pdb=" N ILEc1 68 " --> pdb=" O VALc1 64 " (cutoff:3.500A) Processing helix chain 'c2' and resid 3 through 37 Processing helix chain 'c2' and resid 40 through 72 removed outlier: 4.290A pdb=" N LEUc2 58 " --> pdb=" O LEUc2 54 " (cutoff:3.500A) Proline residue: c2 59 - end of helix Processing helix chain 'c3' and resid 3 through 37 Processing helix chain 'c3' and resid 40 through 72 removed outlier: 4.372A pdb=" N LEUc3 58 " --> pdb=" O LEUc3 54 " (cutoff:3.500A) Proline residue: c3 59 - end of helix removed outlier: 3.635A pdb=" N GLYc3 71 " --> pdb=" O PHEc3 67 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARGc3 72 " --> pdb=" O ILEc3 68 " (cutoff:3.500A) Processing helix chain 'c4' and resid 3 through 37 Processing helix chain 'c4' and resid 40 through 56 removed outlier: 3.665A pdb=" N LEUc4 44 " --> pdb=" O LEUc4 40 " (cutoff:3.500A) Processing helix chain 'c4' and resid 56 through 72 removed outlier: 3.504A pdb=" N ILEc4 60 " --> pdb=" O GLUc4 56 " (cutoff:3.500A) Processing helix chain 'c5' and resid 3 through 37 Processing helix chain 'c5' and resid 40 through 71 removed outlier: 4.938A pdb=" N LEUc5 58 " --> pdb=" O LEUc5 54 " (cutoff:3.500A) Proline residue: c5 59 - end of helix Processing helix chain 'c6' and resid 3 through 37 removed outlier: 3.525A pdb=" N GLNc6 37 " --> pdb=" O GLYc6 33 " (cutoff:3.500A) Processing helix chain 'c6' and resid 40 through 71 removed outlier: 3.827A pdb=" N THRc6 47 " --> pdb=" O VALc6 43 " (cutoff:3.500A) Proline residue: c6 59 - end of helix Processing helix chain 'B' and resid 4 through 24 removed outlier: 4.820A pdb=" N SER B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.719A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 251 Proline residue: B 239 - end of helix removed outlier: 4.042A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.907A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.507A pdb=" N ALA B 285 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.520A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.713A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.794A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.619A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 495 through 498 Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.589A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.547A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.891A pdb=" N HIS C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.614A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 237 through 251 removed outlier: 3.993A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.753A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.732A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 374 through 393 removed outlier: 5.047A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 409 through 421 removed outlier: 4.180A pdb=" N ARG C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.663A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 478 removed outlier: 3.574A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.618A pdb=" N ALA C 490 " --> pdb=" O ASP C 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.647A pdb=" N GLN A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.512A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.570A pdb=" N ASN A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.607A pdb=" N HIS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.877A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.567A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 4.016A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.505A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.817A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.637A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.963A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 397 removed outlier: 3.993A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.607A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.515A pdb=" N LEU A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.657A pdb=" N LEU E 128 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.183A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 removed outlier: 3.719A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU E 267 " --> pdb=" O GLU E 263 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.568A pdb=" N TYR E 277 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 removed outlier: 3.520A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 339 removed outlier: 3.520A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 379 Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 396 through 410 removed outlier: 3.940A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 458 through 469 removed outlier: 3.629A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 179 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 206 through 209 removed outlier: 3.856A pdb=" N SER F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 209' Processing helix chain 'F' and resid 221 through 227 removed outlier: 3.812A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 242 removed outlier: 3.902A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.532A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 308 through 312 removed outlier: 3.603A pdb=" N ASP F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.610A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 removed outlier: 3.546A pdb=" N ALA F 336 " --> pdb=" O GLU F 332 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 388 removed outlier: 4.554A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.505A pdb=" N LYS F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 458 through 469 removed outlier: 3.607A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.913A pdb=" N THR D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 194 through 206 WARNING: missing atoms! Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.619A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.705A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.948A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.565A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.533A pdb=" N TYR D 364 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 removed outlier: 4.197A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER D 411 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.734A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'G' and resid 3 through 58 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.900A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.617A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.602A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 283 removed outlier: 3.522A pdb=" N ILE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 89 through 131 removed outlier: 3.738A pdb=" N ALA H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 21 Processing helix chain 'I' and resid 23 through 41 removed outlier: 3.596A pdb=" N ASN I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 49 removed outlier: 4.265A pdb=" N SER I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 66 Processing helix chain 'I' and resid 70 through 83 Processing helix chain 'I' and resid 85 through 87 No H-bonds generated for 'chain 'I' and resid 85 through 87' Processing helix chain 'I' and resid 88 through 105 Processing helix chain 'I' and resid 118 through 134 removed outlier: 4.293A pdb=" N GLN I 131 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS I 132 " --> pdb=" O VAL I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 176 removed outlier: 3.661A pdb=" N LEU I 169 " --> pdb=" O VAL I 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 43 removed outlier: 3.607A pdb=" N THR B 91 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.340A pdb=" N VAL B 256 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU B 316 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR B 260 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N GLN B 341 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N GLY B 360 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 343 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.519A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.869A pdb=" N GLN C 24 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 162 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER I 113 " --> pdb=" O ILE I 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.187A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 76 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY C 61 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.951A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.120A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C 196 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU C 316 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR C 260 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.523A pdb=" N ILE C 159 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.398A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'A' and resid 107 through 108 removed outlier: 3.547A pdb=" N VAL A 319 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 10 removed outlier: 6.373A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.101A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.312A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 4 through 10 removed outlier: 5.536A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.018A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL F 188 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.712A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.343A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 114 through 118 removed outlier: 6.326A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.273A pdb=" N GLU G 204 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE H 4 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP H 19 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL H 6 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU H 17 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL H 8 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 23 through 24 removed outlier: 3.942A pdb=" N ARG H 51 " --> pdb=" O SER H 24 " (cutoff:3.500A) 2210 hydrogen bonds defined for protein. 6501 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: 8.02 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5934 1.31 - 1.43: 8455 1.43 - 1.56: 20990 1.56 - 1.69: 18 1.69 - 1.81: 191 Bond restraints: 35588 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.36e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.51e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 ... (remaining 35583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 47848 4.01 - 8.01: 429 8.01 - 12.02: 60 12.02 - 16.03: 6 16.03 - 20.04: 3 Bond angle restraints: 48346 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 119.83 20.04 1.00e+00 1.00e+00 4.01e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 123.48 16.39 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 121.07 15.76 1.00e+00 1.00e+00 2.48e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 122.40 14.43 1.00e+00 1.00e+00 2.08e+02 ... (remaining 48341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 20833 21.85 - 43.70: 602 43.70 - 65.54: 39 65.54 - 87.39: 26 87.39 - 109.24: 1 Dihedral angle restraints: 21501 sinusoidal: 8120 harmonic: 13381 Sorted by residual: dihedral pdb=" CA ASP G 136 " pdb=" C ASP G 136 " pdb=" N ILE G 137 " pdb=" CA ILE G 137 " ideal model delta harmonic sigma weight residual -180.00 -141.76 -38.24 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA ASP E 394 " pdb=" C ASP E 394 " pdb=" N GLU E 395 " pdb=" CA GLU E 395 " ideal model delta harmonic sigma weight residual -180.00 -146.38 -33.62 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA SER A 400 " pdb=" C SER A 400 " pdb=" N ASP A 401 " pdb=" CA ASP A 401 " ideal model delta harmonic sigma weight residual 180.00 146.81 33.19 0 5.00e+00 4.00e-02 4.41e+01 ... (remaining 21498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5013 0.095 - 0.189: 730 0.189 - 0.284: 38 0.284 - 0.378: 4 0.378 - 0.473: 2 Chirality restraints: 5787 Sorted by residual: chirality pdb=" CA TYR F 277 " pdb=" N TYR F 277 " pdb=" C TYR F 277 " pdb=" CB TYR F 277 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CG LEU C 313 " pdb=" CB LEU C 313 " pdb=" CD1 LEU C 313 " pdb=" CD2 LEU C 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 5784 not shown) Planarity restraints: 6254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEUc8 58 " 0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PROc8 59 " -0.133 5.00e-02 4.00e+02 pdb=" CA PROc8 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PROc8 59 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUc0 58 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PROc0 59 " 0.129 5.00e-02 4.00e+02 pdb=" CA PROc0 59 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROc0 59 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLNc6 37 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PROc6 38 " -0.127 5.00e-02 4.00e+02 pdb=" CA PROc6 38 " 0.038 5.00e-02 4.00e+02 pdb=" CD PROc6 38 " 0.040 5.00e-02 4.00e+02 ... (remaining 6251 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.69: 6 1.69 - 2.49: 175 2.49 - 3.30: 39034 3.30 - 4.10: 88910 4.10 - 4.90: 165919 Warning: very small nonbonded interaction distances. Nonbonded interactions: 294044 Sorted by model distance: nonbonded pdb=" OE2 GLUc5 39 " pdb=" O PRO H 36 " model vdw 0.890 3.040 nonbonded pdb=" CD GLUc5 39 " pdb=" O PRO H 36 " model vdw 0.895 3.270 nonbonded pdb=" OE2 GLUc5 39 " pdb=" C PRO H 36 " model vdw 1.394 3.270 nonbonded pdb=" OH TYR E 277 " pdb=" OD2 ASP E 315 " model vdw 1.587 3.040 nonbonded pdb=" O PHEc3 65 " pdb=" CD1 TYRc3 69 " model vdw 1.610 3.340 ... (remaining 294039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 8 through 18 and (name N or name CA or name C or name O o \ r name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name CB )) or resid 40 through 352 or (resid 353 and (name N or name CA o \ r name C or name CB or name CG1 or name CG2)) or resid 354 through 393 or (resid \ 394 and (name N or name CA or name C or name CB )) or resid 395 through 396 or \ (resid 397 through 398 and (name N or name CA or name C or name O or name CB )) \ or resid 399 through 402 or (resid 403 through 408 and (name N or name CA or nam \ e C or name O or name CB )) or resid 409 through 450 or (resid 451 and (name N o \ r name CA or name C or name O or name CB )) or resid 452 through 484 or (resid 4 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 486 through \ 495 or (resid 496 and (name N or name CA or name C or name O or name CB )) or r \ esid 497 through 601)) selection = (chain 'B' and ((resid 8 through 18 and (name N or name CA or name C or name O o \ r name CB )) or resid 19 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 352 or (resid 353 and (name N o \ r name CA or name C or name CB or name CG1 or name CG2)) or resid 354 through 39 \ 6 or (resid 397 through 398 and (name N or name CA or name C or name O or name C \ B )) or resid 399 through 405 or (resid 406 through 408 and (name N or name CA o \ r name C or name O or name CB )) or resid 409 through 450 or (resid 451 and (nam \ e N or name CA or name C or name O or name CB )) or resid 452 through 484 or (re \ sid 485 and (name N or name CA or name C or name O or name CB )) or resid 486 th \ rough 495 or (resid 496 and (name N or name CA or name C or name O or name CB )) \ or resid 497 through 601)) selection = (chain 'C' and (resid 8 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 38 or (resid 39 and (name N or name \ CA or name C or name CB )) or resid 40 through 187 or (resid 188 and (name N or \ name CA or name C or name O or name CB )) or resid 189 through 393 or (resid 39 \ 4 and (name N or name CA or name C or name CB )) or resid 395 through 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 381 or (resid 382 and (name N or \ name CA or name C or name O or name CB )) or resid 383 through 388 or (resid 38 \ 9 through 392 and (name N or name CA or name C or name O or name CB )) or resid \ 393 or (resid 394 through 397 and (name N or name CA or name C or name O or name \ CB )) or resid 398 through 430 or (resid 431 and (name N or name CA or name C o \ r name O or name CB )) or resid 432 through 468 or (resid 469 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 34 or (resid 35 through 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 130 or (res \ id 131 and (name N or name CA or name C or name O or name CB )) or resid 132 thr \ ough 195 or (resid 196 and (name N or name CA or name C or name CB or name CG or \ name OD1 or name ND2)) or resid 197 through 208 or (resid 209 and (name N or na \ me CA or name C or name CB or name OG )) or resid 210 through 296 or (resid 297 \ and (name N or name CA or name C or name CB or name CG or name CD or name CE or \ name NZ )) or resid 298 through 381 or (resid 382 and (name N or name CA or name \ C or name O or name CB )) or resid 383 through 388 or (resid 389 through 392 an \ d (name N or name CA or name C or name O or name CB )) or resid 393 or (resid 39 \ 4 through 397 and (name N or name CA or name C or name O or name CB )) or resid \ 398 through 420 or (resid 421 and (name N or name CA or name C or name CB or nam \ e OG1 or name CG2)) or (resid 422 and (name N or name CA or name C )) or resid 4 \ 23 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 468 or (resid 469 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'F' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 34 or (resid 35 through 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 195 or (res \ id 196 and (name N or name CA or name C or name CB or name CG or name OD1 or nam \ e ND2)) or resid 197 through 208 or (resid 209 and (name N or name CA or name C \ or name CB or name OG )) or resid 210 through 296 or (resid 297 and (name N or n \ ame CA or name C or name CB or name CG or name CD or name CE or name NZ )) or re \ sid 298 through 420 or (resid 421 and (name N or name CA or name C or name CB or \ name OG1 or name CG2)) or (resid 422 and (name N or name CA or name C )) or res \ id 423 through 469)) } ncs_group { reference = (chain 'b1' and ((resid 7 and (name N or name CA or name C or name O or name CB \ )) or resid 8 through 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43 or (resid 44 through 140 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'b2' and (resid 7 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 140)) } ncs_group { reference = chain 'c0' selection = chain 'c1' selection = chain 'c2' selection = chain 'c3' selection = chain 'c4' selection = chain 'c5' selection = chain 'c6' selection = chain 'c7' selection = chain 'c8' selection = chain 'c9' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.310 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 0.008 0.117 35589 Z= 0.348 Angle : 1.079 20.037 48346 Z= 0.614 Chirality : 0.063 0.473 5787 Planarity : 0.008 0.077 6254 Dihedral : 10.697 109.241 12921 Min Nonbonded Distance : 0.890 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 0.51 % Allowed : 5.60 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.11), residues: 4642 helix: -1.31 (0.09), residues: 2505 sheet: -1.18 (0.21), residues: 569 loop : -1.96 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 225 TYR 0.034 0.003 TYRc7 69 PHE 0.043 0.004 PHEc3 65 TRP 0.023 0.002 TRP a 206 HIS 0.020 0.002 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00762 (35588) covalent geometry : angle 1.07884 (48346) hydrogen bonds : bond 0.14905 ( 2210) hydrogen bonds : angle 6.71759 ( 6501) Misc. bond : bond 0.00748 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 729 time to evaluate : 1.421 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 TARDY: cannot create tardy model for: "VAL C 353 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 223 MET cc_start: 0.8843 (tmm) cc_final: 0.8618 (tmm) REVERT: B 93 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7311 (mtp180) REVERT: B 219 ASP cc_start: 0.8011 (m-30) cc_final: 0.7591 (m-30) REVERT: B 373 LYS cc_start: 0.7813 (ttmp) cc_final: 0.7466 (tttm) REVERT: B 454 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8066 (mtp180) REVERT: B 496 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7836 (mmpt) REVERT: C 67 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7308 (mm-30) REVERT: C 89 ARG cc_start: 0.7840 (ptt-90) cc_final: 0.7619 (ptp-170) REVERT: C 118 LEU cc_start: 0.8978 (mt) cc_final: 0.8766 (mp) REVERT: C 245 MET cc_start: 0.8626 (mtt) cc_final: 0.8294 (mtt) REVERT: C 354 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8380 (mtt180) REVERT: C 409 LYS cc_start: 0.8111 (mptm) cc_final: 0.7834 (mptp) REVERT: C 426 GLN cc_start: 0.8097 (mt0) cc_final: 0.7479 (pt0) REVERT: C 458 LYS cc_start: 0.8195 (ttpm) cc_final: 0.7955 (tttp) REVERT: A 181 ASP cc_start: 0.7406 (t0) cc_final: 0.7065 (t0) REVERT: A 250 MET cc_start: 0.8839 (ttp) cc_final: 0.8532 (ttp) REVERT: E 205 SER cc_start: 0.8135 (m) cc_final: 0.7850 (m) REVERT: E 218 MET cc_start: 0.8939 (mtt) cc_final: 0.8703 (mtt) REVERT: E 277 TYR cc_start: 0.7027 (m-80) cc_final: 0.6666 (m-80) REVERT: E 332 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6630 (mm-30) REVERT: E 334 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7566 (tttm) REVERT: E 365 GLN cc_start: 0.8039 (pt0) cc_final: 0.7731 (pt0) REVERT: E 464 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6771 (tp30) REVERT: F 127 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7595 (mt-10) REVERT: F 413 ASN cc_start: 0.8906 (p0) cc_final: 0.8540 (p0) REVERT: F 432 GLU cc_start: 0.7095 (mp0) cc_final: 0.6769 (mp0) REVERT: D 3 ARG cc_start: 0.7570 (mtt90) cc_final: 0.7221 (mtt90) REVERT: D 40 ASN cc_start: 0.8784 (m-40) cc_final: 0.8577 (m110) REVERT: D 334 LYS cc_start: 0.8822 (tmtp) cc_final: 0.8616 (tttm) REVERT: G 46 MET cc_start: 0.8773 (tpt) cc_final: 0.7932 (tpt) REVERT: G 151 GLU cc_start: 0.6883 (pm20) cc_final: 0.6392 (mp0) REVERT: G 174 HIS cc_start: 0.8270 (t-90) cc_final: 0.7905 (t-90) REVERT: G 241 MET cc_start: 0.8755 (ttp) cc_final: 0.8488 (ttm) REVERT: I 16 GLN cc_start: 0.7793 (mt0) cc_final: 0.7541 (mt0) REVERT: I 21 GLN cc_start: 0.8068 (mt0) cc_final: 0.7782 (mt0) REVERT: I 141 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6781 (tm-30) outliers start: 18 outliers final: 6 residues processed: 746 average time/residue: 0.7712 time to fit residues: 682.3795 Evaluate side-chains 481 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 473 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 58 PHE Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 31 GLN b1 14 GLN a 16 ASN a 49 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 HIS ** c8 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 23 ASN c4 23 ASN B 186 GLN B 189 GLN B 422 GLN B 425 HIS C 147 GLN C 186 GLN C 433 GLN C 483 ASN A 18 ASN A 46 ASN A 186 GLN A 215 HIS A 333 ASN A 345 GLN A 397 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS E 28 ASN E 330 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 GLN F 28 ASN F 53 HIS F 169 GLN F 196 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 GLN F 401 HIS ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 253 ASN D 324 HIS D 423 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN I 3 GLN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.180898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120623 restraints weight = 37721.738| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.74 r_work: 0.3125 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35589 Z= 0.152 Angle : 0.659 12.147 48346 Z= 0.336 Chirality : 0.046 0.212 5787 Planarity : 0.006 0.107 6254 Dihedral : 6.753 89.078 5187 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 3.66 % Allowed : 11.79 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.12), residues: 4642 helix: 0.18 (0.10), residues: 2509 sheet: -0.89 (0.21), residues: 582 loop : -1.46 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 129 TYR 0.019 0.001 TYRb1 13 PHE 0.025 0.002 PHE a 212 TRP 0.022 0.002 TRP a 206 HIS 0.008 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00340 (35588) covalent geometry : angle 0.65948 (48346) hydrogen bonds : bond 0.04865 ( 2210) hydrogen bonds : angle 4.92900 ( 6501) Misc. bond : bond 0.00422 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 534 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 33 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.4254 (tm) REVERT: a 22 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.4769 (mmt) REVERT: a 119 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8269 (tm) REVERT: a 122 MET cc_start: 0.8855 (ppp) cc_final: 0.8476 (ppp) REVERT: a 160 PHE cc_start: 0.9249 (m-80) cc_final: 0.8782 (m-80) REVERT: a 223 MET cc_start: 0.9420 (tmm) cc_final: 0.8998 (tmm) REVERT: B 53 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8818 (m) REVERT: B 93 ARG cc_start: 0.8430 (mmt-90) cc_final: 0.7377 (mtp180) REVERT: B 219 ASP cc_start: 0.8757 (m-30) cc_final: 0.8284 (m-30) REVERT: B 326 ILE cc_start: 0.8935 (pt) cc_final: 0.8585 (pp) REVERT: B 361 LEU cc_start: 0.8648 (mp) cc_final: 0.8318 (mp) REVERT: B 373 LYS cc_start: 0.7875 (ttmp) cc_final: 0.7498 (tttm) REVERT: B 473 GLU cc_start: 0.7936 (tp30) cc_final: 0.7498 (tp30) REVERT: B 496 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7710 (mmpt) REVERT: B 497 THR cc_start: 0.9148 (m) cc_final: 0.8922 (t) REVERT: C 27 ASP cc_start: 0.8124 (m-30) cc_final: 0.7897 (m-30) REVERT: C 89 ARG cc_start: 0.8385 (ptt-90) cc_final: 0.7883 (ptp-170) REVERT: C 245 MET cc_start: 0.8862 (mtt) cc_final: 0.8605 (mtt) REVERT: C 252 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (mtpm) REVERT: C 313 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8563 (tt) REVERT: C 350 PHE cc_start: 0.8285 (m-80) cc_final: 0.8012 (m-10) REVERT: C 354 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8357 (mtt180) REVERT: C 392 LEU cc_start: 0.7186 (mp) cc_final: 0.6747 (mp) REVERT: C 426 GLN cc_start: 0.8458 (mt0) cc_final: 0.7464 (tm-30) REVERT: C 492 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6929 (mt-10) REVERT: A 19 TYR cc_start: 0.8005 (t80) cc_final: 0.7608 (t80) REVERT: A 250 MET cc_start: 0.9048 (ttp) cc_final: 0.8790 (ttp) REVERT: A 391 GLU cc_start: 0.8537 (tp30) cc_final: 0.8299 (tp30) REVERT: A 397 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8542 (mp-120) REVERT: A 458 LYS cc_start: 0.8121 (ttpm) cc_final: 0.7778 (tttp) REVERT: E 40 ASN cc_start: 0.8662 (m-40) cc_final: 0.8449 (m-40) REVERT: E 135 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8328 (tp) REVERT: E 198 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8296 (tm) REVERT: E 220 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: E 332 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7203 (mm-30) REVERT: E 333 ARG cc_start: 0.7523 (ttm110) cc_final: 0.7259 (ttm110) REVERT: E 334 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7540 (tttm) REVERT: E 365 GLN cc_start: 0.8286 (pt0) cc_final: 0.8008 (pt0) REVERT: F 75 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: F 413 ASN cc_start: 0.8965 (p0) cc_final: 0.8649 (p0) REVERT: F 451 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7859 (t70) REVERT: D 75 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8273 (tp30) REVERT: D 136 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: D 198 LEU cc_start: 0.8296 (tm) cc_final: 0.8077 (tp) REVERT: D 226 MET cc_start: 0.9217 (mtm) cc_final: 0.8986 (mtp) REVERT: D 394 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (t70) REVERT: D 454 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8456 (mtp85) REVERT: G 26 MET cc_start: 0.8367 (mtp) cc_final: 0.8088 (mtp) REVERT: G 33 ASN cc_start: 0.7973 (t0) cc_final: 0.7717 (t0) REVERT: G 46 MET cc_start: 0.8858 (tpt) cc_final: 0.8116 (tpt) REVERT: G 48 LYS cc_start: 0.8003 (tppt) cc_final: 0.7782 (tppt) REVERT: G 151 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: G 174 HIS cc_start: 0.8617 (t-90) cc_final: 0.8201 (t-90) REVERT: G 272 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: H 22 MET cc_start: 0.6988 (tpp) cc_final: 0.6509 (tpp) REVERT: I 16 GLN cc_start: 0.7641 (mt0) cc_final: 0.7399 (mt0) REVERT: I 20 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7852 (mt-10) REVERT: I 23 GLN cc_start: 0.6973 (pt0) cc_final: 0.6627 (pm20) REVERT: I 64 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7711 (pp20) REVERT: I 115 ARG cc_start: 0.7479 (ppp80) cc_final: 0.6858 (mtt180) REVERT: I 139 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6032 (pp20) REVERT: I 141 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6837 (tm-30) REVERT: I 153 ARG cc_start: 0.6492 (ttp80) cc_final: 0.6143 (ttp80) outliers start: 128 outliers final: 34 residues processed: 618 average time/residue: 0.6892 time to fit residues: 515.1661 Evaluate side-chains 529 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 477 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain a residue 22 MET Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain a residue 124 VAL Chi-restraints excluded: chain a residue 171 PHE Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 407 GLN Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 245 optimal weight: 0.6980 chunk 334 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 361 optimal weight: 0.6980 chunk 320 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1 14 GLN a 90 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 113 GLN C 189 GLN C 215 HIS A 18 ASN A 422 GLN E 28 ASN F 28 ASN F 40 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN G 38 ASN G 55 ASN I 21 GLN I 95 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.175589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120022 restraints weight = 38004.719| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.70 r_work: 0.3066 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35589 Z= 0.168 Angle : 0.648 16.810 48346 Z= 0.325 Chirality : 0.046 0.292 5787 Planarity : 0.005 0.081 6254 Dihedral : 6.459 88.738 5177 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 4.11 % Allowed : 13.11 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4642 helix: 0.79 (0.10), residues: 2520 sheet: -0.86 (0.21), residues: 577 loop : -1.18 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGb2 26 TYR 0.022 0.001 TYR G 113 PHE 0.027 0.002 PHE a 212 TRP 0.028 0.002 TRP a 105 HIS 0.010 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00391 (35588) covalent geometry : angle 0.64839 (48346) hydrogen bonds : bond 0.04592 ( 2210) hydrogen bonds : angle 4.65430 ( 6501) Misc. bond : bond 0.00335 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 485 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 40 ARG cc_start: 0.6904 (ttm110) cc_final: 0.6629 (ttm170) REVERT: b1 22 LEU cc_start: 0.8517 (tm) cc_final: 0.8262 (mm) REVERT: a 87 PHE cc_start: 0.8563 (t80) cc_final: 0.8349 (t80) REVERT: a 88 VAL cc_start: 0.9264 (m) cc_final: 0.8936 (m) REVERT: a 119 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8301 (tm) REVERT: a 160 PHE cc_start: 0.9229 (m-80) cc_final: 0.8965 (t80) REVERT: a 170 LEU cc_start: 0.9542 (mt) cc_final: 0.9305 (mp) REVERT: a 223 MET cc_start: 0.9363 (tmm) cc_final: 0.8951 (tmm) REVERT: c4 58 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6130 (tt) REVERT: B 89 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.7420 (mmm-85) REVERT: B 93 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7240 (mtp180) REVERT: B 219 ASP cc_start: 0.8643 (m-30) cc_final: 0.8125 (m-30) REVERT: B 326 ILE cc_start: 0.8878 (pt) cc_final: 0.8549 (pp) REVERT: B 339 ASP cc_start: 0.8219 (m-30) cc_final: 0.7761 (m-30) REVERT: B 373 LYS cc_start: 0.7830 (ttmp) cc_final: 0.7407 (tttm) REVERT: B 483 ASN cc_start: 0.7788 (p0) cc_final: 0.7560 (p0) REVERT: B 486 ASP cc_start: 0.8045 (t70) cc_final: 0.7755 (t0) REVERT: C 27 ASP cc_start: 0.8072 (m-30) cc_final: 0.7762 (m-30) REVERT: C 89 ARG cc_start: 0.8219 (ptt-90) cc_final: 0.7717 (ptp-170) REVERT: C 245 MET cc_start: 0.8756 (mtt) cc_final: 0.8499 (mtt) REVERT: C 313 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8527 (tt) REVERT: C 350 PHE cc_start: 0.8256 (m-80) cc_final: 0.8007 (m-10) REVERT: C 354 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8336 (mtt180) REVERT: C 383 ARG cc_start: 0.6624 (tpt170) cc_final: 0.6417 (tpt170) REVERT: C 426 GLN cc_start: 0.8476 (mt0) cc_final: 0.7355 (pt0) REVERT: C 440 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8641 (tp) REVERT: C 492 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6851 (mt-10) REVERT: A 19 TYR cc_start: 0.7954 (t80) cc_final: 0.7598 (t80) REVERT: A 87 GLU cc_start: 0.8991 (tt0) cc_final: 0.8710 (tp30) REVERT: A 250 MET cc_start: 0.8991 (ttp) cc_final: 0.8791 (ttp) REVERT: A 391 GLU cc_start: 0.8438 (tp30) cc_final: 0.8206 (tp30) REVERT: A 397 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8467 (mp-120) REVERT: E 40 ASN cc_start: 0.8639 (m-40) cc_final: 0.8419 (m-40) REVERT: E 135 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8285 (tp) REVERT: E 198 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8136 (tm) REVERT: E 332 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7120 (mm-30) REVERT: E 333 ARG cc_start: 0.7471 (ttm110) cc_final: 0.7180 (ttm110) REVERT: E 334 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7433 (tttm) REVERT: E 365 GLN cc_start: 0.8040 (pt0) cc_final: 0.7771 (pt0) REVERT: E 432 GLU cc_start: 0.7833 (mp0) cc_final: 0.7563 (mm-30) REVERT: E 464 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6702 (tp30) REVERT: F 135 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8187 (tp) REVERT: F 330 ASN cc_start: 0.8776 (m110) cc_final: 0.8569 (m-40) REVERT: F 376 ARG cc_start: 0.7039 (tpp-160) cc_final: 0.6805 (tpp-160) REVERT: F 451 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7851 (t70) REVERT: D 17 LYS cc_start: 0.8598 (tttt) cc_final: 0.8316 (tttm) REVERT: D 33 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8489 (mt0) REVERT: D 75 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: D 136 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: D 226 MET cc_start: 0.9197 (mtm) cc_final: 0.8969 (mtp) REVERT: D 389 MET cc_start: 0.8718 (mmm) cc_final: 0.8379 (mmm) REVERT: D 394 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8208 (t70) REVERT: D 432 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: D 454 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8389 (mtp85) REVERT: G 26 MET cc_start: 0.8041 (mtp) cc_final: 0.7698 (mtp) REVERT: G 33 ASN cc_start: 0.7893 (t0) cc_final: 0.7654 (t0) REVERT: G 48 LYS cc_start: 0.7899 (tppt) cc_final: 0.7695 (tptm) REVERT: G 174 HIS cc_start: 0.8571 (t-90) cc_final: 0.8176 (t-90) REVERT: G 272 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: H 22 MET cc_start: 0.6960 (tpp) cc_final: 0.6510 (tpp) REVERT: I 16 GLN cc_start: 0.7626 (mt0) cc_final: 0.7359 (mt0) REVERT: I 20 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7878 (mt-10) REVERT: I 21 GLN cc_start: 0.7668 (mt0) cc_final: 0.7448 (mt0) REVERT: I 23 GLN cc_start: 0.7035 (pt0) cc_final: 0.6708 (pm20) REVERT: I 64 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7579 (pp20) REVERT: I 131 GLN cc_start: 0.7362 (mp10) cc_final: 0.7147 (mp10) REVERT: I 139 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6126 (pp20) REVERT: I 141 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6774 (tm-30) outliers start: 144 outliers final: 59 residues processed: 582 average time/residue: 0.7030 time to fit residues: 494.2376 Evaluate side-chains 535 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 461 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 110 THR Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain a residue 124 VAL Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c4 residue 30 THR Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 170 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 186 optimal weight: 0.9990 chunk 252 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 392 optimal weight: 0.5980 chunk 411 optimal weight: 0.7980 chunk 459 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 345 GLN A 488 ASN E 419 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS H 38 HIS I 95 GLN I 142 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.174793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118743 restraints weight = 38044.996| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.69 r_work: 0.3050 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35589 Z= 0.173 Angle : 0.640 18.266 48346 Z= 0.319 Chirality : 0.047 0.315 5787 Planarity : 0.005 0.057 6254 Dihedral : 6.307 82.195 5173 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 3.83 % Allowed : 14.65 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 4642 helix: 1.09 (0.10), residues: 2533 sheet: -0.79 (0.21), residues: 576 loop : -0.98 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 120 TYR 0.023 0.001 TYR B 438 PHE 0.023 0.001 PHE F 250 TRP 0.013 0.001 TRP a 206 HIS 0.010 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00409 (35588) covalent geometry : angle 0.64018 (48346) hydrogen bonds : bond 0.04412 ( 2210) hydrogen bonds : angle 4.52205 ( 6501) Misc. bond : bond 0.00347 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 459 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 33 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4873 (tm) REVERT: b1 22 LEU cc_start: 0.8518 (tm) cc_final: 0.8240 (mm) REVERT: a 87 PHE cc_start: 0.8558 (t80) cc_final: 0.8303 (t80) REVERT: a 119 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8266 (tm) REVERT: a 122 MET cc_start: 0.8285 (ppp) cc_final: 0.8067 (ppp) REVERT: a 160 PHE cc_start: 0.9235 (m-80) cc_final: 0.8971 (t80) REVERT: a 223 MET cc_start: 0.9323 (tmm) cc_final: 0.8925 (tmm) REVERT: c4 58 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6042 (tt) REVERT: B 89 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7431 (mmm-85) REVERT: B 93 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7270 (mtp180) REVERT: B 219 ASP cc_start: 0.8658 (m-30) cc_final: 0.8108 (m-30) REVERT: B 313 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8168 (tt) REVERT: B 326 ILE cc_start: 0.8922 (pt) cc_final: 0.8594 (pp) REVERT: B 373 LYS cc_start: 0.7883 (ttmp) cc_final: 0.7454 (tttm) REVERT: B 483 ASN cc_start: 0.7711 (p0) cc_final: 0.7510 (p0) REVERT: B 486 ASP cc_start: 0.8003 (t70) cc_final: 0.7755 (t0) REVERT: C 27 ASP cc_start: 0.8084 (m-30) cc_final: 0.7728 (m-30) REVERT: C 89 ARG cc_start: 0.8206 (ptt-90) cc_final: 0.7755 (ptp-170) REVERT: C 245 MET cc_start: 0.8762 (mtt) cc_final: 0.8495 (mtt) REVERT: C 313 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 350 PHE cc_start: 0.8238 (m-80) cc_final: 0.7995 (m-10) REVERT: C 354 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8339 (mtt180) REVERT: C 426 GLN cc_start: 0.8475 (mt0) cc_final: 0.7309 (tm-30) REVERT: C 440 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8644 (tp) REVERT: C 492 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6901 (mt-10) REVERT: A 19 TYR cc_start: 0.7908 (t80) cc_final: 0.7549 (t80) REVERT: A 87 GLU cc_start: 0.9017 (tt0) cc_final: 0.8815 (tp30) REVERT: A 391 GLU cc_start: 0.8483 (tp30) cc_final: 0.8167 (tp30) REVERT: A 397 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8569 (mp-120) REVERT: E 40 ASN cc_start: 0.8652 (m-40) cc_final: 0.8424 (m-40) REVERT: E 135 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8300 (tp) REVERT: E 198 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8126 (tm) REVERT: E 332 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7364 (tp30) REVERT: E 334 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7503 (tttm) REVERT: E 365 GLN cc_start: 0.8055 (pt0) cc_final: 0.7782 (pt0) REVERT: E 432 GLU cc_start: 0.7937 (mp0) cc_final: 0.7675 (mm-30) REVERT: E 464 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6616 (tp30) REVERT: F 135 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8242 (tp) REVERT: F 326 ASP cc_start: 0.8389 (m-30) cc_final: 0.8077 (m-30) REVERT: F 330 ASN cc_start: 0.8699 (m110) cc_final: 0.8478 (m-40) REVERT: F 376 ARG cc_start: 0.6989 (tpp-160) cc_final: 0.6640 (tpp-160) REVERT: F 451 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7875 (t70) REVERT: D 17 LYS cc_start: 0.8628 (tttt) cc_final: 0.8362 (tttm) REVERT: D 33 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: D 75 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: D 136 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: D 226 MET cc_start: 0.9217 (mtm) cc_final: 0.8998 (mtp) REVERT: D 389 MET cc_start: 0.8664 (mmm) cc_final: 0.8394 (mmm) REVERT: D 454 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8422 (mtp85) REVERT: G 26 MET cc_start: 0.8092 (mtp) cc_final: 0.7743 (mtp) REVERT: G 33 ASN cc_start: 0.7932 (t0) cc_final: 0.7690 (t0) REVERT: G 46 MET cc_start: 0.8867 (tpt) cc_final: 0.8112 (tpt) REVERT: G 48 LYS cc_start: 0.7895 (tppt) cc_final: 0.7687 (tptm) REVERT: G 174 HIS cc_start: 0.8591 (t-90) cc_final: 0.8212 (t-90) REVERT: G 272 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: H 22 MET cc_start: 0.7001 (tpp) cc_final: 0.6533 (tpp) REVERT: I 16 GLN cc_start: 0.7632 (mt0) cc_final: 0.7392 (mt0) REVERT: I 20 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7892 (mt-10) REVERT: I 21 GLN cc_start: 0.7750 (mt0) cc_final: 0.7520 (mt0) REVERT: I 23 GLN cc_start: 0.6952 (pt0) cc_final: 0.6682 (pm20) REVERT: I 36 GLN cc_start: 0.7854 (tt0) cc_final: 0.7650 (pt0) REVERT: I 64 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8120 (tm-30) REVERT: I 131 GLN cc_start: 0.7602 (mp10) cc_final: 0.7381 (mp10) REVERT: I 139 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6184 (pp20) REVERT: I 141 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6812 (tm-30) outliers start: 134 outliers final: 56 residues processed: 556 average time/residue: 0.6745 time to fit residues: 454.9806 Evaluate side-chains 518 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 447 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c3 residue 6 LEU Chi-restraints excluded: chain c4 residue 58 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 435 optimal weight: 9.9990 chunk 443 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 275 optimal weight: 0.5980 chunk 376 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b1 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN C 113 GLN E 34 HIS E 289 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.176939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118392 restraints weight = 37792.676| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.32 r_work: 0.3082 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35589 Z= 0.178 Angle : 0.645 18.750 48346 Z= 0.319 Chirality : 0.047 0.457 5787 Planarity : 0.005 0.058 6254 Dihedral : 6.189 82.518 5173 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 3.74 % Allowed : 15.59 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.12), residues: 4642 helix: 1.24 (0.10), residues: 2536 sheet: -0.79 (0.21), residues: 578 loop : -0.87 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGb2 26 TYR 0.022 0.001 TYR B 438 PHE 0.021 0.001 PHE a 212 TRP 0.008 0.001 TRP a 206 HIS 0.010 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00425 (35588) covalent geometry : angle 0.64547 (48346) hydrogen bonds : bond 0.04401 ( 2210) hydrogen bonds : angle 4.47013 ( 6501) Misc. bond : bond 0.00333 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 457 time to evaluate : 1.447 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 TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. REVERT: b2 33 LEU cc_start: 0.5211 (OUTLIER) cc_final: 0.4830 (tm) REVERT: b1 22 LEU cc_start: 0.8505 (tm) cc_final: 0.8223 (mm) REVERT: a 119 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8244 (tm) REVERT: a 160 PHE cc_start: 0.9247 (m-80) cc_final: 0.8969 (t80) REVERT: a 223 MET cc_start: 0.9245 (tmm) cc_final: 0.8874 (tmm) REVERT: c7 30 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7482 (m) REVERT: B 89 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7451 (mmm-85) REVERT: B 90 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7241 (ttt90) REVERT: B 93 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7060 (mtp180) REVERT: B 219 ASP cc_start: 0.8705 (m-30) cc_final: 0.8110 (m-30) REVERT: B 313 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8104 (tt) REVERT: B 326 ILE cc_start: 0.8928 (pt) cc_final: 0.8577 (pp) REVERT: B 373 LYS cc_start: 0.7907 (ttmp) cc_final: 0.7460 (tttm) REVERT: B 483 ASN cc_start: 0.7612 (p0) cc_final: 0.7411 (p0) REVERT: C 27 ASP cc_start: 0.8065 (m-30) cc_final: 0.7649 (m-30) REVERT: C 89 ARG cc_start: 0.8115 (ptt-90) cc_final: 0.7651 (ptp-170) REVERT: C 125 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7935 (pt0) REVERT: C 313 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (tt) REVERT: C 354 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8326 (mtt180) REVERT: C 426 GLN cc_start: 0.8449 (mt0) cc_final: 0.7138 (tm-30) REVERT: C 440 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8506 (tp) REVERT: C 492 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6873 (mt-10) REVERT: A 19 TYR cc_start: 0.7849 (t80) cc_final: 0.7516 (t80) REVERT: A 87 GLU cc_start: 0.9108 (tt0) cc_final: 0.8840 (tp30) REVERT: A 181 ASP cc_start: 0.7873 (m-30) cc_final: 0.7531 (m-30) REVERT: A 391 GLU cc_start: 0.8460 (tp30) cc_final: 0.8144 (tp30) REVERT: E 40 ASN cc_start: 0.8515 (m-40) cc_final: 0.8163 (m-40) REVERT: E 198 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7983 (tm) REVERT: E 332 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7400 (tp30) REVERT: E 334 LYS cc_start: 0.7763 (mmtm) cc_final: 0.7274 (tttm) REVERT: E 365 GLN cc_start: 0.7856 (pt0) cc_final: 0.7584 (pt0) REVERT: E 432 GLU cc_start: 0.7932 (mp0) cc_final: 0.7664 (mm-30) REVERT: E 464 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6462 (tp30) REVERT: F 190 GLU cc_start: 0.7268 (tp30) cc_final: 0.6493 (pm20) REVERT: F 201 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7762 (mt-10) REVERT: F 326 ASP cc_start: 0.8359 (m-30) cc_final: 0.8088 (m-30) REVERT: F 376 ARG cc_start: 0.6827 (tpp-160) cc_final: 0.6407 (tpp-160) REVERT: F 451 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7870 (t70) REVERT: D 17 LYS cc_start: 0.8477 (tttt) cc_final: 0.8181 (tttm) REVERT: D 33 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: D 75 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: D 136 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: D 226 MET cc_start: 0.9243 (mtm) cc_final: 0.9035 (mtp) REVERT: D 389 MET cc_start: 0.8649 (mmm) cc_final: 0.8441 (mmm) REVERT: D 394 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8115 (t70) REVERT: D 454 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8385 (mtp85) REVERT: G 26 MET cc_start: 0.7916 (mtp) cc_final: 0.7538 (mtp) REVERT: G 33 ASN cc_start: 0.7809 (t0) cc_final: 0.7568 (t0) REVERT: G 46 MET cc_start: 0.8794 (tpt) cc_final: 0.7983 (tpt) REVERT: G 48 LYS cc_start: 0.7820 (tppt) cc_final: 0.7601 (tptm) REVERT: G 174 HIS cc_start: 0.8498 (t-90) cc_final: 0.8065 (t-90) REVERT: G 272 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: H 22 MET cc_start: 0.6927 (tpp) cc_final: 0.6441 (tpp) REVERT: I 16 GLN cc_start: 0.7500 (mt0) cc_final: 0.7295 (mt0) REVERT: I 20 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7981 (mt-10) REVERT: I 21 GLN cc_start: 0.7593 (mt0) cc_final: 0.7356 (mt0) REVERT: I 23 GLN cc_start: 0.6784 (pt0) cc_final: 0.6517 (pm20) REVERT: I 139 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6122 (pp20) REVERT: I 141 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6802 (tm-30) REVERT: I 171 ARG cc_start: 0.7989 (ptp-110) cc_final: 0.7705 (mtt180) outliers start: 131 outliers final: 63 residues processed: 553 average time/residue: 0.6895 time to fit residues: 461.4553 Evaluate side-chains 516 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 439 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c8 residue 6 LEU Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c2 residue 58 LEU Chi-restraints excluded: chain c3 residue 6 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 170 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 439 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 183 optimal weight: 0.5980 chunk 205 optimal weight: 0.0770 chunk 94 optimal weight: 7.9990 chunk 431 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 248 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1 14 GLN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 422 GLN C 113 GLN E 169 GLN E 419 GLN F 40 ASN F 259 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.181376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124075 restraints weight = 37710.824| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.70 r_work: 0.3123 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 35589 Z= 0.126 Angle : 0.605 16.154 48346 Z= 0.299 Chirality : 0.045 0.321 5787 Planarity : 0.004 0.060 6254 Dihedral : 5.895 81.798 5173 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 3.43 % Allowed : 16.33 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.12), residues: 4642 helix: 1.45 (0.10), residues: 2541 sheet: -0.68 (0.21), residues: 579 loop : -0.71 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGb2 26 TYR 0.013 0.001 TYR B 438 PHE 0.039 0.001 PHE a 212 TRP 0.011 0.001 TRP a 206 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00282 (35588) covalent geometry : angle 0.60528 (48346) hydrogen bonds : bond 0.04051 ( 2210) hydrogen bonds : angle 4.35033 ( 6501) Misc. bond : bond 0.00262 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 485 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 33 LEU cc_start: 0.5218 (OUTLIER) cc_final: 0.4824 (tm) REVERT: b1 22 LEU cc_start: 0.8493 (tm) cc_final: 0.8208 (mm) REVERT: a 25 ILE cc_start: 0.6318 (pt) cc_final: 0.6052 (pp) REVERT: a 160 PHE cc_start: 0.9250 (m-80) cc_final: 0.8976 (t80) REVERT: a 223 MET cc_start: 0.9203 (tmm) cc_final: 0.8776 (tmm) REVERT: a 226 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8883 (mmp) REVERT: B 89 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.7447 (mmm-85) REVERT: B 93 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7170 (mtp180) REVERT: B 219 ASP cc_start: 0.8690 (m-30) cc_final: 0.8167 (m-30) REVERT: B 326 ILE cc_start: 0.8948 (pt) cc_final: 0.8586 (pp) REVERT: B 373 LYS cc_start: 0.7917 (ttmp) cc_final: 0.7457 (tttm) REVERT: B 391 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7734 (tp30) REVERT: C 27 ASP cc_start: 0.8065 (m-30) cc_final: 0.7685 (m-30) REVERT: C 40 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.8021 (mtp-110) REVERT: C 89 ARG cc_start: 0.8120 (ptt-90) cc_final: 0.7655 (ptp-170) REVERT: C 125 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7816 (pt0) REVERT: C 248 TYR cc_start: 0.8877 (t80) cc_final: 0.8552 (t80) REVERT: C 313 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8483 (tt) REVERT: C 350 PHE cc_start: 0.8138 (m-80) cc_final: 0.7892 (m-10) REVERT: C 354 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8343 (mtt180) REVERT: C 392 LEU cc_start: 0.7176 (mp) cc_final: 0.6713 (mp) REVERT: C 426 GLN cc_start: 0.8445 (mt0) cc_final: 0.7191 (tm-30) REVERT: C 440 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8476 (tp) REVERT: C 492 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6867 (mt-10) REVERT: A 19 TYR cc_start: 0.7809 (t80) cc_final: 0.7418 (t80) REVERT: A 87 GLU cc_start: 0.9067 (tt0) cc_final: 0.8841 (tp30) REVERT: A 181 ASP cc_start: 0.7883 (m-30) cc_final: 0.7531 (m-30) REVERT: A 391 GLU cc_start: 0.8410 (tp30) cc_final: 0.8115 (tp30) REVERT: E 40 ASN cc_start: 0.8455 (m-40) cc_final: 0.8207 (m-40) REVERT: E 198 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7986 (tm) REVERT: E 332 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7103 (mm-30) REVERT: E 334 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7259 (tttm) REVERT: E 365 GLN cc_start: 0.7927 (pt0) cc_final: 0.7651 (pt0) REVERT: E 419 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: E 432 GLU cc_start: 0.7943 (mp0) cc_final: 0.7695 (mm-30) REVERT: E 464 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6476 (tp30) REVERT: F 190 GLU cc_start: 0.7118 (tp30) cc_final: 0.6624 (pm20) REVERT: F 201 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7700 (mt-10) REVERT: F 202 MET cc_start: 0.8464 (mtt) cc_final: 0.8231 (mtt) REVERT: F 217 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: F 326 ASP cc_start: 0.8391 (m-30) cc_final: 0.8068 (m-30) REVERT: F 376 ARG cc_start: 0.6878 (tpp-160) cc_final: 0.6442 (tpp-160) REVERT: F 451 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7561 (t70) REVERT: D 17 LYS cc_start: 0.8516 (tttt) cc_final: 0.8239 (tttm) REVERT: D 33 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: D 75 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: D 270 ARG cc_start: 0.9016 (mtt180) cc_final: 0.8546 (mtt180) REVERT: D 394 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (t70) REVERT: D 454 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8412 (mtp85) REVERT: G 26 MET cc_start: 0.8017 (mtp) cc_final: 0.7659 (mtp) REVERT: G 46 MET cc_start: 0.8844 (tpt) cc_final: 0.8064 (tpt) REVERT: G 48 LYS cc_start: 0.7751 (tppt) cc_final: 0.7541 (tptm) REVERT: G 174 HIS cc_start: 0.8481 (t-90) cc_final: 0.8108 (t-90) REVERT: G 272 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: H 22 MET cc_start: 0.6987 (tpp) cc_final: 0.6542 (tpp) REVERT: I 20 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7967 (mt-10) REVERT: I 21 GLN cc_start: 0.7571 (mt0) cc_final: 0.7334 (mt0) REVERT: I 23 GLN cc_start: 0.6750 (pt0) cc_final: 0.6480 (pm20) REVERT: I 64 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7597 (pp20) REVERT: I 139 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6124 (pp20) REVERT: I 141 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6781 (tm-30) outliers start: 120 outliers final: 58 residues processed: 566 average time/residue: 0.6854 time to fit residues: 469.4648 Evaluate side-chains 523 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 452 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 226 MET Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c2 residue 58 LEU Chi-restraints excluded: chain c3 residue 6 LEU Chi-restraints excluded: chain c5 residue 37 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 170 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 435 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 29 optimal weight: 30.0000 chunk 283 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 413 optimal weight: 7.9990 chunk 397 optimal weight: 0.9980 chunk 202 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1 14 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 422 GLN C 113 GLN A 18 ASN E 33 GLN E 169 GLN F 40 ASN F 259 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123438 restraints weight = 37705.195| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.35 r_work: 0.3115 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35589 Z= 0.149 Angle : 0.624 17.069 48346 Z= 0.307 Chirality : 0.045 0.343 5787 Planarity : 0.004 0.058 6254 Dihedral : 5.860 79.751 5173 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 3.51 % Allowed : 16.93 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4642 helix: 1.53 (0.10), residues: 2533 sheet: -0.65 (0.21), residues: 579 loop : -0.66 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 5 TYR 0.017 0.001 TYR B 438 PHE 0.029 0.001 PHE a 212 TRP 0.012 0.001 TRP a 206 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00348 (35588) covalent geometry : angle 0.62377 (48346) hydrogen bonds : bond 0.04109 ( 2210) hydrogen bonds : angle 4.33100 ( 6501) Misc. bond : bond 0.00287 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 464 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.8957 (tttm) cc_final: 0.8513 (mmpt) REVERT: b2 33 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4878 (tm) REVERT: b1 22 LEU cc_start: 0.8482 (tm) cc_final: 0.8207 (mm) REVERT: a 25 ILE cc_start: 0.6291 (pt) cc_final: 0.6033 (pp) REVERT: a 119 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8222 (tm) REVERT: a 160 PHE cc_start: 0.9197 (m-80) cc_final: 0.8944 (t80) REVERT: B 93 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.7221 (mtp180) REVERT: B 219 ASP cc_start: 0.8654 (m-30) cc_final: 0.8092 (m-30) REVERT: B 326 ILE cc_start: 0.8960 (pt) cc_final: 0.8593 (pp) REVERT: B 373 LYS cc_start: 0.7916 (ttmp) cc_final: 0.7387 (tttm) REVERT: B 391 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7757 (tp30) REVERT: C 27 ASP cc_start: 0.8063 (m-30) cc_final: 0.7685 (m-30) REVERT: C 40 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8124 (mtp-110) REVERT: C 89 ARG cc_start: 0.8102 (ptt-90) cc_final: 0.7644 (ptp-170) REVERT: C 236 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7442 (t80) REVERT: C 313 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8553 (tt) REVERT: C 350 PHE cc_start: 0.8140 (m-80) cc_final: 0.7863 (m-10) REVERT: C 354 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8354 (mtt180) REVERT: C 392 LEU cc_start: 0.7213 (mp) cc_final: 0.6735 (mp) REVERT: C 426 GLN cc_start: 0.8451 (mt0) cc_final: 0.7196 (tm-30) REVERT: C 440 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8494 (tp) REVERT: C 483 ASN cc_start: 0.7589 (t0) cc_final: 0.7364 (t0) REVERT: C 492 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6942 (mt-10) REVERT: A 19 TYR cc_start: 0.7908 (t80) cc_final: 0.7549 (t80) REVERT: A 87 GLU cc_start: 0.9080 (tt0) cc_final: 0.8857 (tp30) REVERT: A 181 ASP cc_start: 0.7867 (m-30) cc_final: 0.7540 (m-30) REVERT: A 391 GLU cc_start: 0.8391 (tp30) cc_final: 0.8102 (tp30) REVERT: E 40 ASN cc_start: 0.8455 (m-40) cc_final: 0.8184 (m-40) REVERT: E 198 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8059 (tm) REVERT: E 332 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7375 (tp30) REVERT: E 334 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7281 (tttm) REVERT: E 365 GLN cc_start: 0.7973 (pt0) cc_final: 0.7700 (pt0) REVERT: E 419 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: E 432 GLU cc_start: 0.7964 (mp0) cc_final: 0.7713 (mm-30) REVERT: E 464 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6513 (tp30) REVERT: F 190 GLU cc_start: 0.7331 (tp30) cc_final: 0.6688 (pm20) REVERT: F 201 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7717 (mt-10) REVERT: F 217 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: F 233 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7968 (tp) REVERT: F 326 ASP cc_start: 0.8303 (m-30) cc_final: 0.7995 (m-30) REVERT: F 451 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7592 (t70) REVERT: D 17 LYS cc_start: 0.8536 (tttt) cc_final: 0.8246 (tttm) REVERT: D 33 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: D 75 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: D 365 GLN cc_start: 0.8042 (mp-120) cc_final: 0.7556 (mp-120) REVERT: D 454 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8416 (mtp85) REVERT: G 26 MET cc_start: 0.7996 (mtp) cc_final: 0.7641 (mtp) REVERT: G 46 MET cc_start: 0.8798 (tpt) cc_final: 0.8006 (tpt) REVERT: G 48 LYS cc_start: 0.7762 (tppt) cc_final: 0.7548 (tptm) REVERT: G 174 HIS cc_start: 0.8501 (t-90) cc_final: 0.8134 (t-90) REVERT: G 272 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: H 22 MET cc_start: 0.7117 (tpp) cc_final: 0.6675 (tpp) REVERT: I 20 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8060 (mt-10) REVERT: I 21 GLN cc_start: 0.7737 (mt0) cc_final: 0.7430 (mt0) REVERT: I 23 GLN cc_start: 0.6934 (pt0) cc_final: 0.6451 (pm20) REVERT: I 139 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6150 (pp20) REVERT: I 141 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6787 (tm-30) outliers start: 123 outliers final: 67 residues processed: 551 average time/residue: 0.6800 time to fit residues: 452.7492 Evaluate side-chains 529 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 448 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain a residue 124 VAL Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c3 residue 6 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 170 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 158 optimal weight: 2.9990 chunk 461 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 422 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 14 GLN ** b1 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 113 GLN A 18 ASN E 419 GLN F 40 ASN F 259 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 40 ASN I 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118406 restraints weight = 37886.856| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.49 r_work: 0.3082 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35589 Z= 0.184 Angle : 0.664 18.363 48346 Z= 0.325 Chirality : 0.047 0.411 5787 Planarity : 0.005 0.057 6254 Dihedral : 5.960 80.160 5173 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 3.23 % Allowed : 17.36 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.12), residues: 4642 helix: 1.51 (0.10), residues: 2534 sheet: -0.67 (0.21), residues: 579 loop : -0.68 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 5 TYR 0.030 0.001 TYR B 438 PHE 0.022 0.001 PHE B 456 TRP 0.012 0.001 TRP a 206 HIS 0.009 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00442 (35588) covalent geometry : angle 0.66424 (48346) hydrogen bonds : bond 0.04256 ( 2210) hydrogen bonds : angle 4.37755 ( 6501) Misc. bond : bond 0.00345 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 448 time to evaluate : 1.347 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 TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 33 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4911 (tm) REVERT: a 119 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8272 (tm) REVERT: a 160 PHE cc_start: 0.9204 (m-80) cc_final: 0.8953 (t80) REVERT: a 180 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8800 (pp) REVERT: B 89 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8438 (mmm160) REVERT: B 93 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.7272 (mtp180) REVERT: B 137 MET cc_start: 0.8833 (mpp) cc_final: 0.8319 (mpm) REVERT: B 219 ASP cc_start: 0.8720 (m-30) cc_final: 0.8140 (m-30) REVERT: B 313 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 326 ILE cc_start: 0.8908 (pt) cc_final: 0.8530 (pp) REVERT: B 391 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7836 (tp30) REVERT: B 426 GLN cc_start: 0.8505 (mt0) cc_final: 0.8115 (mt0) REVERT: C 89 ARG cc_start: 0.8154 (ptt-90) cc_final: 0.7699 (ptp-110) REVERT: C 236 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7561 (t80) REVERT: C 313 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8575 (tt) REVERT: C 426 GLN cc_start: 0.8450 (mt0) cc_final: 0.7214 (tm-30) REVERT: C 440 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8537 (tp) REVERT: C 483 ASN cc_start: 0.7668 (t0) cc_final: 0.7330 (t0) REVERT: C 492 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6841 (mt-10) REVERT: A 19 TYR cc_start: 0.7928 (t80) cc_final: 0.7561 (t80) REVERT: A 87 GLU cc_start: 0.9123 (tt0) cc_final: 0.8850 (tp30) REVERT: A 181 ASP cc_start: 0.7926 (m-30) cc_final: 0.7605 (m-30) REVERT: A 262 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7671 (t0) REVERT: A 391 GLU cc_start: 0.8467 (tp30) cc_final: 0.8167 (tp30) REVERT: E 40 ASN cc_start: 0.8495 (m-40) cc_final: 0.8236 (m-40) REVERT: E 198 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8124 (tm) REVERT: E 332 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7249 (mm-30) REVERT: E 334 LYS cc_start: 0.7834 (mmtm) cc_final: 0.7334 (tttm) REVERT: E 365 GLN cc_start: 0.8007 (pt0) cc_final: 0.7727 (pt0) REVERT: E 432 GLU cc_start: 0.8043 (mp0) cc_final: 0.7777 (mm-30) REVERT: E 464 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6710 (tp30) REVERT: F 190 GLU cc_start: 0.7204 (tp30) cc_final: 0.6649 (pm20) REVERT: F 201 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7733 (mt-10) REVERT: F 217 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: F 233 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8045 (tp) REVERT: F 326 ASP cc_start: 0.8332 (m-30) cc_final: 0.8078 (m-30) REVERT: F 378 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7717 (tppt) REVERT: F 451 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7777 (t70) REVERT: D 17 LYS cc_start: 0.8561 (tttt) cc_final: 0.8264 (tttm) REVERT: D 33 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: D 75 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: D 454 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8450 (mtp85) REVERT: G 26 MET cc_start: 0.7965 (mtp) cc_final: 0.7565 (mtp) REVERT: G 46 MET cc_start: 0.8749 (tpt) cc_final: 0.7961 (tpt) REVERT: G 48 LYS cc_start: 0.7777 (tppt) cc_final: 0.7562 (tptm) REVERT: G 174 HIS cc_start: 0.8566 (t-90) cc_final: 0.8124 (t-90) REVERT: G 272 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: H 22 MET cc_start: 0.7126 (tpp) cc_final: 0.6691 (tpp) REVERT: I 20 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8105 (mt-10) REVERT: I 21 GLN cc_start: 0.7698 (mt0) cc_final: 0.7364 (mt0) REVERT: I 23 GLN cc_start: 0.6913 (pt0) cc_final: 0.6412 (pm20) REVERT: I 139 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6221 (pp20) REVERT: I 141 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6896 (tm-30) outliers start: 113 outliers final: 65 residues processed: 523 average time/residue: 0.6741 time to fit residues: 426.4176 Evaluate side-chains 519 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 437 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c3 residue 6 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 170 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 1 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 378 optimal weight: 3.9990 chunk 132 optimal weight: 0.0170 chunk 22 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 309 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 14 GLN ** b1 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c0 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 113 GLN F 40 ASN F 259 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN I 36 GLN I 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118367 restraints weight = 37695.239| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.50 r_work: 0.3075 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35589 Z= 0.170 Angle : 0.654 17.852 48346 Z= 0.321 Chirality : 0.047 0.452 5787 Planarity : 0.004 0.056 6254 Dihedral : 5.938 84.156 5173 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 3.06 % Allowed : 17.85 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4642 helix: 1.55 (0.10), residues: 2511 sheet: -0.67 (0.21), residues: 580 loop : -0.73 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 5 TYR 0.030 0.001 TYR B 438 PHE 0.029 0.001 PHE a 219 TRP 0.013 0.001 TRP a 206 HIS 0.008 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00405 (35588) covalent geometry : angle 0.65433 (48346) hydrogen bonds : bond 0.04190 ( 2210) hydrogen bonds : angle 4.35960 ( 6501) Misc. bond : bond 0.00327 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 450 time to evaluate : 0.980 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 TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.8900 (tttm) cc_final: 0.8502 (mmpt) REVERT: b2 33 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.4929 (tm) REVERT: a 160 PHE cc_start: 0.9220 (m-80) cc_final: 0.8966 (t80) REVERT: a 180 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8805 (pp) REVERT: B 89 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8398 (mmm-85) REVERT: B 93 ARG cc_start: 0.8302 (mmt-90) cc_final: 0.7212 (mtp180) REVERT: B 137 MET cc_start: 0.8781 (mpp) cc_final: 0.8321 (mpm) REVERT: B 219 ASP cc_start: 0.8722 (m-30) cc_final: 0.8124 (m-30) REVERT: B 373 LYS cc_start: 0.7880 (ttmp) cc_final: 0.7333 (tttm) REVERT: B 391 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7851 (tp30) REVERT: C 89 ARG cc_start: 0.8033 (ptt-90) cc_final: 0.7636 (ptp-110) REVERT: C 236 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7462 (t80) REVERT: C 313 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8558 (tt) REVERT: C 426 GLN cc_start: 0.8433 (mt0) cc_final: 0.7232 (pt0) REVERT: C 440 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8427 (tp) REVERT: C 483 ASN cc_start: 0.7657 (t0) cc_final: 0.7328 (t0) REVERT: C 492 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6829 (mt-10) REVERT: A 19 TYR cc_start: 0.7852 (t80) cc_final: 0.7482 (t80) REVERT: A 28 VAL cc_start: 0.7898 (m) cc_final: 0.7663 (p) REVERT: A 87 GLU cc_start: 0.9130 (tt0) cc_final: 0.8840 (tp30) REVERT: A 181 ASP cc_start: 0.7920 (m-30) cc_final: 0.7644 (m-30) REVERT: A 262 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7581 (t0) REVERT: A 391 GLU cc_start: 0.8457 (tp30) cc_final: 0.8160 (tp30) REVERT: E 17 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8097 (tttm) REVERT: E 40 ASN cc_start: 0.8391 (m-40) cc_final: 0.8138 (m-40) REVERT: E 198 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8098 (tm) REVERT: E 332 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7206 (mm-30) REVERT: E 334 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7267 (tttm) REVERT: E 365 GLN cc_start: 0.7948 (pt0) cc_final: 0.7671 (pt0) REVERT: E 432 GLU cc_start: 0.8024 (mp0) cc_final: 0.7744 (mm-30) REVERT: E 464 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6597 (tp30) REVERT: F 56 ASP cc_start: 0.8299 (t0) cc_final: 0.7853 (t0) REVERT: F 190 GLU cc_start: 0.7139 (tp30) cc_final: 0.6616 (pm20) REVERT: F 201 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7686 (mt-10) REVERT: F 217 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: F 233 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7981 (tp) REVERT: F 256 ARG cc_start: 0.8548 (mpt90) cc_final: 0.7771 (mmp80) REVERT: F 326 ASP cc_start: 0.8365 (m-30) cc_final: 0.8082 (m-30) REVERT: F 378 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7656 (tppt) REVERT: F 451 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7736 (t70) REVERT: D 17 LYS cc_start: 0.8521 (tttt) cc_final: 0.8227 (tttm) REVERT: D 33 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: D 75 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: D 454 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8413 (mtp85) REVERT: G 26 MET cc_start: 0.7924 (mtp) cc_final: 0.7524 (mtp) REVERT: G 46 MET cc_start: 0.8693 (tpt) cc_final: 0.7911 (tpt) REVERT: G 111 ASP cc_start: 0.8410 (t0) cc_final: 0.7943 (p0) REVERT: G 174 HIS cc_start: 0.8484 (t-90) cc_final: 0.8055 (t-90) REVERT: G 272 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: H 22 MET cc_start: 0.7073 (tpp) cc_final: 0.6621 (tpp) REVERT: I 20 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8098 (mt-10) REVERT: I 21 GLN cc_start: 0.7630 (mt0) cc_final: 0.7302 (mt0) REVERT: I 23 GLN cc_start: 0.6839 (pt0) cc_final: 0.6349 (pm20) REVERT: I 139 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6199 (pp20) REVERT: I 141 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6893 (tm-30) outliers start: 107 outliers final: 67 residues processed: 526 average time/residue: 0.6831 time to fit residues: 433.8516 Evaluate side-chains 517 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 435 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b2 residue 25 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 124 VAL Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c3 residue 5 VAL Chi-restraints excluded: chain c3 residue 6 LEU Chi-restraints excluded: chain c5 residue 34 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 170 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 262 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 328 optimal weight: 0.8980 chunk 280 optimal weight: 2.9990 chunk 460 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 chunk 333 optimal weight: 0.6980 chunk 300 optimal weight: 2.9990 chunk 140 optimal weight: 0.0030 chunk 342 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 14 GLN ** b1 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 422 GLN C 42 HIS C 113 GLN E 169 GLN F 40 ASN F 259 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN I 36 GLN I 57 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.179080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118730 restraints weight = 37716.108| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.65 r_work: 0.3115 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35589 Z= 0.131 Angle : 0.644 18.334 48346 Z= 0.312 Chirality : 0.045 0.447 5787 Planarity : 0.004 0.056 6254 Dihedral : 5.789 87.939 5173 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 2.66 % Allowed : 18.48 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.12), residues: 4642 helix: 1.65 (0.10), residues: 2521 sheet: -0.63 (0.21), residues: 585 loop : -0.65 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGb2 26 TYR 0.030 0.001 TYR B 438 PHE 0.024 0.001 PHE a 219 TRP 0.013 0.001 TRP a 206 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00297 (35588) covalent geometry : angle 0.64360 (48346) hydrogen bonds : bond 0.03975 ( 2210) hydrogen bonds : angle 4.29209 ( 6501) Misc. bond : bond 0.00265 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9284 Ramachandran restraints generated. 4642 Oldfield, 0 Emsley, 4642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 449 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR D 421 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b2 27 LYS cc_start: 0.8889 (tttm) cc_final: 0.8503 (mmpt) REVERT: b2 33 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.4917 (tm) REVERT: a 160 PHE cc_start: 0.9239 (m-80) cc_final: 0.8988 (t80) REVERT: a 180 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8801 (pp) REVERT: B 89 ARG cc_start: 0.8621 (mmm160) cc_final: 0.8381 (mmm-85) REVERT: B 93 ARG cc_start: 0.8255 (mmt-90) cc_final: 0.7125 (mtp180) REVERT: B 137 MET cc_start: 0.8809 (mpp) cc_final: 0.8301 (mpm) REVERT: B 219 ASP cc_start: 0.8709 (m-30) cc_final: 0.8115 (m-30) REVERT: B 375 MET cc_start: 0.8274 (tpt) cc_final: 0.8030 (tpp) REVERT: B 391 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7809 (tp30) REVERT: C 89 ARG cc_start: 0.8048 (ptt-90) cc_final: 0.7643 (ptp-110) REVERT: C 313 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8505 (tt) REVERT: C 350 PHE cc_start: 0.8082 (m-80) cc_final: 0.7860 (m-10) REVERT: C 426 GLN cc_start: 0.8424 (mt0) cc_final: 0.7155 (tm-30) REVERT: C 440 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8418 (tp) REVERT: C 483 ASN cc_start: 0.7689 (t0) cc_final: 0.7381 (t160) REVERT: C 492 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6794 (mt-10) REVERT: A 19 TYR cc_start: 0.7835 (t80) cc_final: 0.7459 (t80) REVERT: A 87 GLU cc_start: 0.9111 (tt0) cc_final: 0.8849 (tp30) REVERT: A 137 MET cc_start: 0.8598 (mmp) cc_final: 0.8386 (mpm) REVERT: A 181 ASP cc_start: 0.7884 (m-30) cc_final: 0.7600 (m-30) REVERT: A 218 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 262 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7508 (t0) REVERT: A 391 GLU cc_start: 0.8432 (tp30) cc_final: 0.8150 (tp30) REVERT: E 17 LYS cc_start: 0.8534 (ttmm) cc_final: 0.8096 (tttm) REVERT: E 40 ASN cc_start: 0.8387 (m-40) cc_final: 0.8164 (m-40) REVERT: E 198 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7979 (tm) REVERT: E 332 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7080 (mm-30) REVERT: E 334 LYS cc_start: 0.7730 (mmtm) cc_final: 0.7203 (tttm) REVERT: E 365 GLN cc_start: 0.7948 (pt0) cc_final: 0.7666 (pt0) REVERT: E 432 GLU cc_start: 0.8001 (mp0) cc_final: 0.7715 (mm-30) REVERT: E 464 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6539 (tp30) REVERT: F 56 ASP cc_start: 0.8293 (t0) cc_final: 0.7814 (t0) REVERT: F 190 GLU cc_start: 0.7227 (tp30) cc_final: 0.6629 (pm20) REVERT: F 201 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7583 (mt-10) REVERT: F 217 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: F 233 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7929 (tp) REVERT: F 256 ARG cc_start: 0.8469 (mpt90) cc_final: 0.7719 (mmp80) REVERT: F 326 ASP cc_start: 0.8343 (m-30) cc_final: 0.8055 (m-30) REVERT: F 451 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7196 (t0) REVERT: D 17 LYS cc_start: 0.8500 (tttt) cc_final: 0.8218 (tttm) REVERT: D 75 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: D 270 ARG cc_start: 0.9030 (mtt180) cc_final: 0.8608 (mtt180) REVERT: D 365 GLN cc_start: 0.8145 (mp-120) cc_final: 0.7881 (mm110) REVERT: D 454 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8390 (mtp85) REVERT: G 26 MET cc_start: 0.7968 (mtp) cc_final: 0.7617 (mtp) REVERT: G 46 MET cc_start: 0.8720 (tpt) cc_final: 0.7877 (tpt) REVERT: G 111 ASP cc_start: 0.8428 (t0) cc_final: 0.7954 (p0) REVERT: G 174 HIS cc_start: 0.8453 (t-90) cc_final: 0.8072 (t-90) REVERT: G 272 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: H 22 MET cc_start: 0.7072 (tpp) cc_final: 0.6662 (tpp) REVERT: I 20 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8085 (mt-10) REVERT: I 21 GLN cc_start: 0.7652 (mt0) cc_final: 0.7307 (mt0) REVERT: I 23 GLN cc_start: 0.6895 (pt0) cc_final: 0.6378 (pm20) REVERT: I 36 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7808 (pp30) REVERT: I 64 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7838 (pp20) REVERT: I 139 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6179 (pp20) REVERT: I 141 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6867 (tm-30) outliers start: 93 outliers final: 60 residues processed: 516 average time/residue: 0.6908 time to fit residues: 431.0380 Evaluate side-chains 507 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 433 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 22 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 180 LEU Chi-restraints excluded: chain c8 residue 61 ILE Chi-restraints excluded: chain c8 residue 67 PHE Chi-restraints excluded: chain c1 residue 5 VAL Chi-restraints excluded: chain c1 residue 67 PHE Chi-restraints excluded: chain c2 residue 58 LEU Chi-restraints excluded: chain c3 residue 6 LEU Chi-restraints excluded: chain c5 residue 34 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 454 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 170 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 326 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 443 optimal weight: 7.9990 chunk 219 optimal weight: 0.0070 chunk 366 optimal weight: 3.9990 chunk 137 optimal weight: 0.0060 chunk 190 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 0.7416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b2 14 GLN ** b1 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 422 GLN C 113 GLN E 169 GLN F 40 ASN F 259 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN I 36 GLN I 57 GLN I 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.178874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119436 restraints weight = 37653.517| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.74 r_work: 0.3114 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 35589 Z= 0.168 Angle : 0.735 59.193 48346 Z= 0.380 Chirality : 0.047 0.961 5787 Planarity : 0.004 0.056 6254 Dihedral : 5.787 87.950 5173 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 2.48 % Allowed : 19.05 % Favored : 78.47 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.12), residues: 4642 helix: 1.65 (0.10), residues: 2521 sheet: -0.62 (0.21), residues: 585 loop : -0.65 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 5 TYR 0.025 0.001 TYR B 438 PHE 0.020 0.001 PHE B 456 TRP 0.012 0.001 TRP a 206 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00385 (35588) covalent geometry : angle 0.73510 (48346) hydrogen bonds : bond 0.03989 ( 2210) hydrogen bonds : angle 4.29045 ( 6501) Misc. bond : bond 0.00269 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14505.55 seconds wall clock time: 246 minutes 55.46 seconds (14815.46 seconds total)