Starting phenix.real_space_refine on Sun Jul 5 13:20:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tax_25789/07_2026/7tax_25789.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 459 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 33 5.16 5 C 17215 2.51 5 N 5054 2.21 5 O 5455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27855 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 9, 'ARG:plan': 9, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "X" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 5.67, per 1000 atoms: 0.20 Number of scatterers: 27855 At special positions: 0 Unit cell: (130.2, 178.5, 152.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 98 15.00 O 5455 8.00 N 5054 7.00 C 17215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 939.2 milliseconds 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6226 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 55 sheets defined 35.1% alpha, 21.0% beta 18 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.518A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.508A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.743A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.667A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.808A pdb=" N TRP A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 4.018A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 341 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.551A pdb=" N ALA A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.021A pdb=" N LEU A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.176A pdb=" N THR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.934A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.904A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.801A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.638A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.586A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.773A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.949A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.547A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 58 removed outlier: 5.265A pdb=" N GLN E 56 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.549A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.555A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN F 56 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU F 57 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.673A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.629A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 332 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 172 removed outlier: 6.503A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.519A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 191 through 197 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 3.515A pdb=" N ASP K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 199 Processing helix chain 'K' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.423A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.351A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.541A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.727A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 61 removed outlier: 3.852A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.838A pdb=" N PHE D 355 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.969A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.764A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC2, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.804A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.185A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 176 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL E 177 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP E 196 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'E' and resid 63 through 70 removed outlier: 3.627A pdb=" N GLY E 70 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC8, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.723A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.530A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA F 176 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.519A pdb=" N GLN F 96 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.695A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.210A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.585A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE3, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.692A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 196 removed outlier: 5.000A pdb=" N VAL H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG H 185 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER H 262 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR H 97 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR H 264 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP H 99 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE8, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.754A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.511A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.282A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.964A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.560A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 38 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR J 32 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF6, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.700A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 85 through 90 removed outlier: 5.232A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.256A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 85 through 91 Processing sheet with id=AG1, first strand: chain 'K' and resid 99 through 100 1159 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4483 1.30 - 1.43: 7939 1.43 - 1.56: 15980 1.56 - 1.68: 195 1.68 - 1.81: 52 Bond restraints: 28649 Sorted by residual: bond pdb=" CA ALA G 271 " pdb=" C ALA G 271 " ideal model delta sigma weight residual 1.521 1.455 0.066 1.19e-02 7.06e+03 3.06e+01 bond pdb=" C HIS G 159 " pdb=" O HIS G 159 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.66e+01 bond pdb=" CA HIS G 159 " pdb=" C HIS G 159 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.29e-02 6.01e+03 1.63e+01 bond pdb=" CA ARG G 269 " pdb=" C ARG G 269 " ideal model delta sigma weight residual 1.530 1.474 0.055 1.44e-02 4.82e+03 1.48e+01 bond pdb=" C ALA G 158 " pdb=" O ALA G 158 " ideal model delta sigma weight residual 1.236 1.189 0.048 1.25e-02 6.40e+03 1.45e+01 ... (remaining 28644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 38797 2.34 - 4.68: 524 4.68 - 7.02: 53 7.02 - 9.36: 10 9.36 - 11.69: 2 Bond angle restraints: 39386 Sorted by residual: angle pdb=" N LEU G 161 " pdb=" CA LEU G 161 " pdb=" C LEU G 161 " ideal model delta sigma weight residual 114.04 102.35 11.69 1.24e+00 6.50e-01 8.89e+01 angle pdb=" O SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 123.33 130.37 -7.04 1.21e+00 6.83e-01 3.39e+01 angle pdb=" C LEU G 161 " pdb=" N ALA G 162 " pdb=" CA ALA G 162 " ideal model delta sigma weight residual 120.68 111.67 9.01 1.70e+00 3.46e-01 2.81e+01 angle pdb=" N ILE D 286 " pdb=" CA ILE D 286 " pdb=" C ILE D 286 " ideal model delta sigma weight residual 113.20 108.23 4.97 9.60e-01 1.09e+00 2.68e+01 angle pdb=" CA SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 116.01 108.52 7.49 1.51e+00 4.39e-01 2.46e+01 ... (remaining 39381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 16519 35.90 - 71.81: 369 71.81 - 107.71: 29 107.71 - 143.62: 1 143.62 - 179.52: 5 Dihedral angle restraints: 16923 sinusoidal: 7277 harmonic: 9646 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 55.78 144.22 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 57.83 142.17 1 1.50e+01 4.44e-03 7.64e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 52.48 179.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3609 0.051 - 0.103: 668 0.103 - 0.154: 143 0.154 - 0.205: 10 0.205 - 0.257: 2 Chirality restraints: 4432 Sorted by residual: chirality pdb=" CA ASP G 270 " pdb=" N ASP G 270 " pdb=" C ASP G 270 " pdb=" CB ASP G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 301 " pdb=" CA THR A 301 " pdb=" OG1 THR A 301 " pdb=" CG2 THR A 301 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 4429 not shown) Planarity restraints: 4823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 72 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 267 " 0.013 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C SER G 267 " -0.051 2.00e-02 2.50e+03 pdb=" O SER G 267 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL G 268 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 364 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 365 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.041 5.00e-02 4.00e+02 ... (remaining 4820 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4673 2.77 - 3.30: 25724 3.30 - 3.83: 48928 3.83 - 4.37: 59225 4.37 - 4.90: 98107 Nonbonded interactions: 236657 Sorted by model distance: nonbonded pdb=" OH TYR A 179 " pdb=" OD2 ASP B 272 " model vdw 2.236 3.040 nonbonded pdb=" O VAL K 170 " pdb=" OG1 THR K 177 " model vdw 2.243 3.040 nonbonded pdb=" O GLY J 172 " pdb=" OG SER J 175 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.268 3.040 ... (remaining 236652 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.37 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.500 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 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 : 0.003 0.066 28649 Z= 0.211 Angle : 0.677 11.694 39386 Z= 0.395 Chirality : 0.043 0.257 4432 Planarity : 0.005 0.077 4823 Dihedral : 15.161 179.523 10697 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 3322 helix: -0.02 (0.14), residues: 1078 sheet: 0.76 (0.21), residues: 540 loop : -1.58 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 191 TYR 0.039 0.002 TYR G 304 PHE 0.023 0.001 PHE A 16 TRP 0.017 0.001 TRP G 49 HIS 0.009 0.001 HIS K 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.21 (28649) covalent geometry : angle 0.67739 / 0.39 (39386) hydrogen bonds : bond 0.18486 / 12.88 ( 1176) hydrogen bonds : angle 7.24627 / 5.11 ( 3238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 866 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.6915 (mm) cc_final: 0.6584 (mt) REVERT: B 121 HIS cc_start: 0.5778 (m90) cc_final: 0.5508 (m-70) REVERT: D 276 SER cc_start: 0.6268 (m) cc_final: 0.6013 (t) REVERT: J 28 TRP cc_start: 0.5319 (m100) cc_final: 0.4436 (m100) outliers start: 0 outliers final: 5 residues processed: 866 average time/residue: 0.5009 time to fit residues: 516.8098 Evaluate side-chains 506 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 501 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain I residue 170 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 129 ASN A 253 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 393 ASN A 416 GLN B 18 GLN B 21 ASN B 69 GLN B 89 ASN B 104 HIS B 168 GLN B 293 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 170 ASN D 281 ASN E 316 GLN F 186 GLN F 242 GLN G 102 ASN G 160 ASN G 163 ASN G 260 GLN G 319 GLN H 96 GLN H 242 GLN H 348 ASN I 146 ASN I 281 ASN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.150448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102626 restraints weight = 45592.781| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.74 r_work: 0.3202 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 28649 Z= 0.290 Angle : 0.887 12.297 39386 Z= 0.467 Chirality : 0.051 0.476 4432 Planarity : 0.007 0.087 4823 Dihedral : 14.129 179.657 4818 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.22 % Allowed : 15.61 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3322 helix: 0.10 (0.15), residues: 1052 sheet: 0.61 (0.21), residues: 566 loop : -1.45 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.002 ARG H 191 TYR 0.029 0.003 TYR F 324 PHE 0.033 0.003 PHE B 284 TRP 0.042 0.003 TRP H 193 HIS 0.017 0.002 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.29 (28649) covalent geometry : angle 0.88708 / 0.47 (39386) hydrogen bonds : bond 0.04852 / 3.36 ( 1176) hydrogen bonds : angle 5.60683 / 3.92 ( 3238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 586 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.6858 (tppp) cc_final: 0.6609 (tppp) REVERT: A 102 ASP cc_start: 0.7707 (p0) cc_final: 0.7481 (p0) REVERT: A 174 LEU cc_start: 0.8093 (mm) cc_final: 0.7891 (mt) REVERT: A 200 HIS cc_start: 0.7910 (t-90) cc_final: 0.7502 (t-90) REVERT: A 208 GLU cc_start: 0.8216 (tp30) cc_final: 0.7984 (tp30) REVERT: A 256 ASN cc_start: 0.6289 (t0) cc_final: 0.6045 (t0) REVERT: A 264 LEU cc_start: 0.7694 (mp) cc_final: 0.7424 (mt) REVERT: A 283 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8399 (t-90) REVERT: A 289 HIS cc_start: 0.8852 (m170) cc_final: 0.8545 (m170) REVERT: A 296 GLU cc_start: 0.7535 (tp30) cc_final: 0.7318 (tp30) REVERT: A 299 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8020 (ttp80) REVERT: A 300 LEU cc_start: 0.8229 (mm) cc_final: 0.7316 (mt) REVERT: A 321 ARG cc_start: 0.7406 (tpm170) cc_final: 0.5916 (tpm-80) REVERT: A 329 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6828 (mp) REVERT: B 72 GLN cc_start: 0.8077 (pt0) cc_final: 0.7408 (tt0) REVERT: B 121 HIS cc_start: 0.6284 (m90) cc_final: 0.5653 (m-70) REVERT: B 159 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6353 (tt) REVERT: B 218 ARG cc_start: 0.7082 (ptt180) cc_final: 0.6516 (ptt180) REVERT: B 284 PHE cc_start: 0.7675 (m-80) cc_final: 0.7403 (m-80) REVERT: C 112 LEU cc_start: 0.0697 (tp) cc_final: 0.0354 (mm) REVERT: E 143 THR cc_start: 0.8590 (t) cc_final: 0.8281 (p) REVERT: E 168 TRP cc_start: 0.8386 (m100) cc_final: 0.8156 (m100) REVERT: E 206 LYS cc_start: 0.7878 (mtpp) cc_final: 0.7645 (pttp) REVERT: E 312 LYS cc_start: 0.8361 (ptpt) cc_final: 0.7936 (pttt) REVERT: F 139 GLN cc_start: 0.8176 (tp40) cc_final: 0.7888 (tt0) REVERT: F 188 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6518 (pm20) REVERT: G 144 TYR cc_start: 0.7817 (t80) cc_final: 0.7584 (t80) REVERT: G 155 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7381 (ttp-110) REVERT: G 168 TRP cc_start: 0.8040 (m100) cc_final: 0.7812 (m100) REVERT: H 185 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7229 (ttm-80) REVERT: H 186 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7052 (mp-120) REVERT: H 254 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7703 (tttt) REVERT: H 335 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: I 113 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6430 (ttm-80) REVERT: I 136 LYS cc_start: 0.8558 (tptm) cc_final: 0.8264 (tptp) REVERT: I 203 ARG cc_start: 0.6301 (ptp-110) cc_final: 0.5918 (mtp-110) REVERT: I 324 TYR cc_start: 0.6433 (m-10) cc_final: 0.6091 (m-10) REVERT: J 28 TRP cc_start: 0.7781 (m100) cc_final: 0.7422 (m100) REVERT: J 37 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8136 (tpp) REVERT: J 81 ASP cc_start: 0.5870 (t0) cc_final: 0.5634 (t70) REVERT: J 109 TYR cc_start: 0.7077 (m-80) cc_final: 0.6857 (m-80) REVERT: K 4 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6368 (tp) REVERT: K 36 GLU cc_start: 0.7518 (tt0) cc_final: 0.7134 (tt0) REVERT: K 54 GLU cc_start: 0.6713 (tm-30) cc_final: 0.5762 (tm-30) REVERT: K 61 GLU cc_start: 0.8314 (pt0) cc_final: 0.7989 (pp20) REVERT: K 69 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.7477 (mtm110) REVERT: K 166 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6289 (pt0) REVERT: K 176 PHE cc_start: 0.7088 (m-80) cc_final: 0.6733 (m-10) REVERT: K 209 LYS cc_start: 0.7705 (tppt) cc_final: 0.7490 (tppp) outliers start: 110 outliers final: 27 residues processed: 656 average time/residue: 0.4983 time to fit residues: 390.2024 Evaluate side-chains 470 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 59 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 136 optimal weight: 0.0870 chunk 218 optimal weight: 0.9990 chunk 304 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 81 ASN A 83 HIS ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 324 GLN B 293 HIS C 19 GLN D 170 ASN E 96 GLN F 248 GLN G 260 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN G 343 HIS H 96 GLN I 96 GLN I 242 GLN J 27 GLN J 216 HIS K 5 HIS K 25 HIS K 216 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.150567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100323 restraints weight = 54303.855| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.79 r_work: 0.3209 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 28649 Z= 0.152 Angle : 0.662 10.345 39386 Z= 0.343 Chirality : 0.043 0.439 4432 Planarity : 0.005 0.075 4823 Dihedral : 13.888 178.487 4810 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.49 % Allowed : 19.40 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3322 helix: 0.72 (0.15), residues: 1064 sheet: 0.70 (0.21), residues: 562 loop : -1.44 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 306 TYR 0.021 0.002 TYR D 133 PHE 0.023 0.002 PHE A 118 TRP 0.018 0.001 TRP A 155 HIS 0.006 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (28649) covalent geometry : angle 0.66250 / 0.34 (39386) hydrogen bonds : bond 0.03912 / 2.74 ( 1176) hydrogen bonds : angle 5.11926 / 3.61 ( 3238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 449 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7620 (p0) cc_final: 0.7381 (p0) REVERT: A 111 ASN cc_start: 0.7030 (t0) cc_final: 0.6751 (t0) REVERT: A 123 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4191 (tp) REVERT: A 220 GLU cc_start: 0.8363 (tt0) cc_final: 0.7854 (tm-30) REVERT: A 283 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.8030 (t-90) REVERT: A 296 GLU cc_start: 0.7680 (tp30) cc_final: 0.6749 (tp30) REVERT: A 299 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7970 (ttp80) REVERT: A 300 LEU cc_start: 0.8108 (mm) cc_final: 0.7065 (mt) REVERT: A 306 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7167 (ttp80) REVERT: A 321 ARG cc_start: 0.7209 (tpm170) cc_final: 0.6694 (tpm-80) REVERT: A 332 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6105 (mp0) REVERT: A 393 ASN cc_start: 0.8754 (t0) cc_final: 0.8537 (t0) REVERT: B 38 THR cc_start: 0.7232 (m) cc_final: 0.6973 (p) REVERT: B 72 GLN cc_start: 0.8075 (pt0) cc_final: 0.7467 (tt0) REVERT: B 121 HIS cc_start: 0.6188 (m90) cc_final: 0.5616 (m-70) REVERT: B 180 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8486 (pp) REVERT: B 197 LEU cc_start: 0.8018 (tp) cc_final: 0.7783 (tm) REVERT: B 218 ARG cc_start: 0.6993 (ptt180) cc_final: 0.6448 (ptt180) REVERT: B 268 ARG cc_start: 0.5966 (tpt-90) cc_final: 0.5741 (tpt-90) REVERT: C 112 LEU cc_start: 0.0841 (tp) cc_final: 0.0522 (mm) REVERT: D 354 VAL cc_start: 0.8366 (t) cc_final: 0.8145 (t) REVERT: E 206 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7748 (pttp) REVERT: F 80 ASP cc_start: 0.8749 (t0) cc_final: 0.8440 (t0) REVERT: F 97 THR cc_start: 0.8817 (m) cc_final: 0.8569 (t) REVERT: F 139 GLN cc_start: 0.8172 (tp40) cc_final: 0.7932 (tt0) REVERT: F 188 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6590 (pm20) REVERT: F 270 ASP cc_start: 0.8410 (p0) cc_final: 0.7881 (m-30) REVERT: F 320 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7691 (mmmt) REVERT: G 65 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7968 (mm-30) REVERT: G 155 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7411 (ttp-170) REVERT: G 203 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6326 (mtp-110) REVERT: H 143 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8306 (p) REVERT: H 185 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7288 (ttm-80) REVERT: H 186 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7173 (mp10) REVERT: H 335 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: I 96 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: I 113 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6704 (ttm-80) REVERT: I 203 ARG cc_start: 0.6276 (ptp-110) cc_final: 0.5745 (mtp85) REVERT: J 54 GLU cc_start: 0.8289 (tp30) cc_final: 0.8048 (tp30) REVERT: J 81 ASP cc_start: 0.5833 (t0) cc_final: 0.5633 (t0) REVERT: K 36 GLU cc_start: 0.7309 (tt0) cc_final: 0.6939 (tt0) REVERT: K 54 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5652 (tm-30) REVERT: K 61 GLU cc_start: 0.8336 (pt0) cc_final: 0.7961 (pp20) REVERT: K 127 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7983 (pt0) REVERT: K 176 PHE cc_start: 0.7178 (m-80) cc_final: 0.6882 (m-10) REVERT: K 209 LYS cc_start: 0.7875 (tppt) cc_final: 0.7579 (tppp) outliers start: 117 outliers final: 32 residues processed: 521 average time/residue: 0.5185 time to fit residues: 321.7937 Evaluate side-chains 431 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 388 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 309 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 240 optimal weight: 0.7980 chunk 256 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 200 HIS A 253 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN E 348 ASN F 160 ASN F 248 GLN F 343 HIS ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN I 281 ASN J 19 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.149694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099891 restraints weight = 47649.005| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.59 r_work: 0.3183 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28649 Z= 0.147 Angle : 0.637 10.325 39386 Z= 0.329 Chirality : 0.042 0.349 4432 Planarity : 0.004 0.069 4823 Dihedral : 13.781 178.563 4810 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.22 % Allowed : 19.82 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3322 helix: 0.96 (0.15), residues: 1066 sheet: 0.71 (0.21), residues: 560 loop : -1.42 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 52 TYR 0.017 0.002 TYR E 144 PHE 0.026 0.002 PHE A 118 TRP 0.015 0.001 TRP A 155 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (28649) covalent geometry : angle 0.63749 / 0.33 (39386) hydrogen bonds : bond 0.03378 / 2.37 ( 1176) hydrogen bonds : angle 4.93406 / 3.48 ( 3238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 422 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7784 (p0) cc_final: 0.7520 (p0) REVERT: A 208 GLU cc_start: 0.8276 (tp30) cc_final: 0.7967 (tp30) REVERT: A 220 GLU cc_start: 0.8315 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 281 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6148 (mmp) REVERT: A 283 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.8113 (t-90) REVERT: A 296 GLU cc_start: 0.7643 (tp30) cc_final: 0.6868 (tp30) REVERT: A 299 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8101 (ttp80) REVERT: A 300 LEU cc_start: 0.8227 (mm) cc_final: 0.7152 (mt) REVERT: A 306 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6900 (ttp80) REVERT: A 321 ARG cc_start: 0.7231 (tpm170) cc_final: 0.6398 (tpm-80) REVERT: A 324 GLN cc_start: 0.6854 (pt0) cc_final: 0.6598 (pt0) REVERT: A 329 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6912 (mp) REVERT: A 332 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: A 397 ARG cc_start: 0.8581 (ttm110) cc_final: 0.8242 (mtt180) REVERT: A 422 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7381 (tt) REVERT: B 72 GLN cc_start: 0.8075 (pt0) cc_final: 0.7611 (tt0) REVERT: B 121 HIS cc_start: 0.6116 (m90) cc_final: 0.5590 (m-70) REVERT: B 197 LEU cc_start: 0.8182 (tp) cc_final: 0.7926 (tm) REVERT: B 218 ARG cc_start: 0.7128 (ptt180) cc_final: 0.6638 (ptt180) REVERT: C 102 ARG cc_start: 0.3461 (ttt180) cc_final: 0.2812 (ptp90) REVERT: C 112 LEU cc_start: 0.0936 (tp) cc_final: 0.0539 (mm) REVERT: D 302 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: D 354 VAL cc_start: 0.8526 (t) cc_final: 0.8287 (t) REVERT: E 65 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7279 (mm-30) REVERT: E 143 THR cc_start: 0.8652 (t) cc_final: 0.8387 (p) REVERT: E 206 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7818 (pttp) REVERT: F 80 ASP cc_start: 0.8848 (t0) cc_final: 0.8470 (t0) REVERT: F 117 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.6892 (mtp85) REVERT: F 139 GLN cc_start: 0.8446 (tp40) cc_final: 0.8104 (tt0) REVERT: F 188 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6706 (pm20) REVERT: F 270 ASP cc_start: 0.8405 (p0) cc_final: 0.7869 (m-30) REVERT: F 320 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7773 (mmmt) REVERT: G 65 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8281 (mm-30) REVERT: G 155 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7484 (ttp-170) REVERT: G 203 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6494 (mtp-110) REVERT: H 143 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8253 (p) REVERT: H 185 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7479 (ttm-80) REVERT: H 186 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7476 (tp40) REVERT: H 335 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: I 113 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6999 (ttm-80) REVERT: I 203 ARG cc_start: 0.6429 (ptp-110) cc_final: 0.6115 (mtp-110) REVERT: I 206 LYS cc_start: 0.7613 (mtmm) cc_final: 0.7408 (mtmm) REVERT: I 324 TYR cc_start: 0.7037 (m-10) cc_final: 0.6660 (m-10) REVERT: J 54 GLU cc_start: 0.8455 (tp30) cc_final: 0.8149 (tp30) REVERT: J 81 ASP cc_start: 0.6242 (t0) cc_final: 0.5918 (t0) REVERT: J 134 GLU cc_start: 0.8219 (pp20) cc_final: 0.7886 (pp20) REVERT: K 54 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6238 (tm-30) REVERT: K 61 GLU cc_start: 0.8340 (pt0) cc_final: 0.8019 (pp20) REVERT: K 88 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8326 (pmm-80) REVERT: K 134 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: K 173 GLU cc_start: 0.6478 (tp30) cc_final: 0.6232 (mm-30) REVERT: K 209 LYS cc_start: 0.8024 (tppt) cc_final: 0.7706 (tppp) outliers start: 110 outliers final: 33 residues processed: 488 average time/residue: 0.5218 time to fit residues: 302.6992 Evaluate side-chains 407 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 88 ARG Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 260 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 85 optimal weight: 0.0070 chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 257 optimal weight: 0.5980 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 305 HIS D 148 GLN D 170 ASN D 343 HIS F 310 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN I 242 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS K 216 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.149952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099755 restraints weight = 44378.998| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.52 r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28649 Z= 0.146 Angle : 0.622 10.479 39386 Z= 0.319 Chirality : 0.042 0.356 4432 Planarity : 0.004 0.053 4823 Dihedral : 13.629 178.238 4808 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.87 % Allowed : 21.82 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3322 helix: 1.11 (0.16), residues: 1066 sheet: 0.66 (0.21), residues: 566 loop : -1.36 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 185 TYR 0.014 0.002 TYR E 144 PHE 0.015 0.001 PHE B 284 TRP 0.017 0.001 TRP B 247 HIS 0.006 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (28649) covalent geometry : angle 0.62170 / 0.32 (39386) hydrogen bonds : bond 0.03291 / 2.33 ( 1176) hydrogen bonds : angle 4.82601 / 3.41 ( 3238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 382 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7774 (p0) cc_final: 0.7541 (p0) REVERT: A 208 GLU cc_start: 0.8332 (tp30) cc_final: 0.8006 (tp30) REVERT: A 220 GLU cc_start: 0.8375 (tt0) cc_final: 0.7742 (tm-30) REVERT: A 283 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8166 (t-90) REVERT: A 299 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8156 (ttp80) REVERT: A 306 ARG cc_start: 0.7383 (ttp80) cc_final: 0.7078 (ttp80) REVERT: A 321 ARG cc_start: 0.7222 (tpm170) cc_final: 0.6437 (tpm-80) REVERT: A 324 GLN cc_start: 0.6808 (pt0) cc_final: 0.6590 (pt0) REVERT: A 332 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: A 397 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8268 (mtt180) REVERT: A 422 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 427 GLU cc_start: 0.7146 (tp30) cc_final: 0.6912 (tp30) REVERT: B 67 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: B 72 GLN cc_start: 0.8262 (pt0) cc_final: 0.7839 (tt0) REVERT: B 121 HIS cc_start: 0.6232 (m90) cc_final: 0.5789 (m-70) REVERT: B 218 ARG cc_start: 0.7243 (ptt180) cc_final: 0.6814 (ptt180) REVERT: C 102 ARG cc_start: 0.3348 (ttt180) cc_final: 0.2220 (ptm-80) REVERT: C 112 LEU cc_start: 0.0903 (tp) cc_final: 0.0428 (mm) REVERT: C 117 MET cc_start: 0.1055 (ptt) cc_final: 0.0786 (mpp) REVERT: D 354 VAL cc_start: 0.8647 (t) cc_final: 0.8393 (t) REVERT: E 34 GLU cc_start: 0.8384 (tt0) cc_final: 0.8042 (tt0) REVERT: E 65 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7361 (mm-30) REVERT: E 143 THR cc_start: 0.8671 (t) cc_final: 0.8424 (p) REVERT: F 34 GLU cc_start: 0.7970 (tt0) cc_final: 0.7596 (mt-10) REVERT: F 79 LYS cc_start: 0.9193 (ptpt) cc_final: 0.8902 (pptt) REVERT: F 117 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7098 (mtp85) REVERT: F 139 GLN cc_start: 0.8533 (tp40) cc_final: 0.8041 (tt0) REVERT: F 143 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8576 (p) REVERT: F 188 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6912 (pm20) REVERT: F 270 ASP cc_start: 0.8443 (p0) cc_final: 0.7989 (m-30) REVERT: F 320 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7964 (mmtt) REVERT: H 55 SER cc_start: 0.8189 (p) cc_final: 0.7968 (p) REVERT: H 143 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8410 (p) REVERT: H 185 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7640 (ttm-80) REVERT: H 186 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7768 (tp40) REVERT: H 203 ARG cc_start: 0.7377 (mmm-85) cc_final: 0.6892 (mmm160) REVERT: I 113 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7843 (ptm-80) REVERT: I 203 ARG cc_start: 0.6491 (ptp-110) cc_final: 0.6181 (mtp-110) REVERT: I 206 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7488 (mtmm) REVERT: I 324 TYR cc_start: 0.7230 (m-10) cc_final: 0.6944 (m-10) REVERT: J 37 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: J 54 GLU cc_start: 0.8520 (tp30) cc_final: 0.8228 (tp30) REVERT: J 81 ASP cc_start: 0.6558 (t0) cc_final: 0.6232 (t0) REVERT: K 36 GLU cc_start: 0.6994 (tt0) cc_final: 0.6657 (tt0) REVERT: K 37 MET cc_start: 0.6867 (ptm) cc_final: 0.5520 (ppp) REVERT: K 54 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6285 (tm-30) REVERT: K 61 GLU cc_start: 0.8303 (pt0) cc_final: 0.8001 (pp20) REVERT: K 88 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8390 (pmm-80) REVERT: K 134 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: K 173 GLU cc_start: 0.6592 (tp30) cc_final: 0.6391 (mm-30) REVERT: K 209 LYS cc_start: 0.8118 (tppt) cc_final: 0.7804 (tppp) outliers start: 101 outliers final: 40 residues processed: 448 average time/residue: 0.5451 time to fit residues: 289.7733 Evaluate side-chains 400 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 348 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 88 ARG Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 119 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 321 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 282 ASN D 148 GLN ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN G 260 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS J 19 HIS J 194 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS K 208 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.147411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095115 restraints weight = 53650.290| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.77 r_work: 0.3091 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28649 Z= 0.187 Angle : 0.702 14.185 39386 Z= 0.361 Chirality : 0.045 0.366 4432 Planarity : 0.005 0.055 4823 Dihedral : 13.694 178.589 4808 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.68 % Allowed : 21.78 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3322 helix: 0.93 (0.15), residues: 1069 sheet: 0.58 (0.21), residues: 564 loop : -1.33 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 269 TYR 0.022 0.002 TYR E 144 PHE 0.028 0.002 PHE A 20 TRP 0.041 0.002 TRP B 247 HIS 0.006 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (28649) covalent geometry : angle 0.70199 / 0.36 (39386) hydrogen bonds : bond 0.03443 / 2.40 ( 1176) hydrogen bonds : angle 4.82025 / 3.41 ( 3238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 391 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: A 102 ASP cc_start: 0.7853 (p0) cc_final: 0.7611 (p0) REVERT: A 220 GLU cc_start: 0.8410 (tt0) cc_final: 0.7895 (tm-30) REVERT: A 281 MET cc_start: 0.6536 (tpt) cc_final: 0.6321 (mmp) REVERT: A 283 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8138 (t-90) REVERT: A 296 GLU cc_start: 0.8256 (pm20) cc_final: 0.6797 (tp30) REVERT: A 299 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8133 (ptm-80) REVERT: A 300 LEU cc_start: 0.8586 (mt) cc_final: 0.7969 (mt) REVERT: A 306 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7089 (ttp80) REVERT: A 321 ARG cc_start: 0.7207 (tpm170) cc_final: 0.6556 (tpm-80) REVERT: A 324 GLN cc_start: 0.6873 (pt0) cc_final: 0.6421 (pt0) REVERT: A 397 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8281 (mtt180) REVERT: A 420 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8460 (ptmt) REVERT: A 422 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7777 (tt) REVERT: A 427 GLU cc_start: 0.7276 (tp30) cc_final: 0.7075 (tp30) REVERT: B 121 HIS cc_start: 0.6460 (m90) cc_final: 0.5936 (m-70) REVERT: B 132 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: B 171 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7803 (ttpp) REVERT: B 294 ARG cc_start: 0.7080 (mmp80) cc_final: 0.6603 (mpt180) REVERT: C 112 LEU cc_start: 0.0864 (tp) cc_final: 0.0414 (mm) REVERT: D 354 VAL cc_start: 0.8833 (t) cc_final: 0.8567 (t) REVERT: E 34 GLU cc_start: 0.8276 (tt0) cc_final: 0.8061 (tt0) REVERT: E 37 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8216 (mp) REVERT: E 65 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7282 (mm-30) REVERT: E 269 ARG cc_start: 0.8164 (ptp90) cc_final: 0.7876 (mtm-85) REVERT: E 335 GLU cc_start: 0.8220 (tt0) cc_final: 0.7980 (mt-10) REVERT: F 34 GLU cc_start: 0.7978 (tt0) cc_final: 0.7619 (mt-10) REVERT: F 79 LYS cc_start: 0.9034 (ptpt) cc_final: 0.8826 (ptpt) REVERT: F 117 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7403 (mtp85) REVERT: F 188 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7467 (pm20) REVERT: F 301 VAL cc_start: 0.9012 (t) cc_final: 0.8765 (t) REVERT: G 65 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8440 (mm-30) REVERT: G 91 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: G 99 ASP cc_start: 0.8484 (m-30) cc_final: 0.8259 (t0) REVERT: G 159 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7296 (t-90) REVERT: G 203 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7129 (mmm-85) REVERT: G 212 ASP cc_start: 0.8359 (m-30) cc_final: 0.8128 (m-30) REVERT: H 55 SER cc_start: 0.8437 (p) cc_final: 0.8137 (p) REVERT: H 143 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8609 (p) REVERT: H 185 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7733 (ttm-80) REVERT: H 214 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8634 (tt) REVERT: H 318 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7360 (ptmm) REVERT: H 335 GLU cc_start: 0.8394 (pm20) cc_final: 0.8107 (pm20) REVERT: I 78 THR cc_start: 0.7828 (m) cc_final: 0.7568 (p) REVERT: I 113 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8296 (ttt-90) REVERT: I 155 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8018 (ttp80) REVERT: I 206 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7976 (mtmm) REVERT: I 335 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7802 (mt-10) REVERT: J 81 ASP cc_start: 0.7104 (t0) cc_final: 0.6167 (t70) REVERT: J 124 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8194 (p) REVERT: J 208 GLN cc_start: 0.7409 (mt0) cc_final: 0.7100 (mt0) REVERT: J 220 ASP cc_start: 0.8561 (t0) cc_final: 0.8321 (t70) REVERT: K 37 MET cc_start: 0.6868 (ptm) cc_final: 0.5480 (ppp) REVERT: K 54 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: K 61 GLU cc_start: 0.8449 (pt0) cc_final: 0.8111 (pp20) REVERT: K 88 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8446 (ptp90) REVERT: K 134 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: K 155 ASP cc_start: 0.6404 (p0) cc_final: 0.5959 (p0) REVERT: K 157 GLU cc_start: 0.7959 (mp0) cc_final: 0.7553 (pm20) REVERT: K 166 GLU cc_start: 0.7637 (pt0) cc_final: 0.6287 (pm20) REVERT: K 173 GLU cc_start: 0.6829 (tp30) cc_final: 0.6525 (mm-30) REVERT: K 209 LYS cc_start: 0.8133 (tppt) cc_final: 0.7743 (tppp) outliers start: 122 outliers final: 34 residues processed: 472 average time/residue: 0.5762 time to fit residues: 321.3810 Evaluate side-chains 365 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 267 SER Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 88 ARG Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 196 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 274 optimal weight: 0.0980 chunk 124 optimal weight: 9.9990 chunk 157 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN B 282 ASN ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 102 ASN E 146 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.148059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096089 restraints weight = 53865.758| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.72 r_work: 0.3110 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.7892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28649 Z= 0.134 Angle : 0.630 12.116 39386 Z= 0.322 Chirality : 0.042 0.336 4432 Planarity : 0.004 0.053 4823 Dihedral : 13.644 178.043 4808 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.26 % Allowed : 23.96 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3322 helix: 1.13 (0.16), residues: 1071 sheet: 0.44 (0.21), residues: 595 loop : -1.26 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 52 TYR 0.015 0.001 TYR F 304 PHE 0.027 0.001 PHE A 16 TRP 0.032 0.001 TRP B 247 HIS 0.004 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (28649) covalent geometry : angle 0.63008 / 0.32 (39386) hydrogen bonds : bond 0.03177 / 2.21 ( 1176) hydrogen bonds : angle 4.73515 / 3.34 ( 3238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 327 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6553 (tppt) cc_final: 0.6350 (tppt) REVERT: A 74 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7450 (t-90) REVERT: A 102 ASP cc_start: 0.7992 (p0) cc_final: 0.7777 (p0) REVERT: A 220 GLU cc_start: 0.8519 (tt0) cc_final: 0.7795 (tm-30) REVERT: A 242 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8331 (mmmt) REVERT: A 281 MET cc_start: 0.6575 (tpt) cc_final: 0.6373 (mmp) REVERT: A 283 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8122 (t-90) REVERT: A 300 LEU cc_start: 0.8715 (mt) cc_final: 0.8246 (mt) REVERT: A 306 ARG cc_start: 0.7468 (ttp80) cc_final: 0.7120 (ttp80) REVERT: A 321 ARG cc_start: 0.7224 (tpm170) cc_final: 0.6594 (tpm-80) REVERT: A 324 GLN cc_start: 0.6999 (pt0) cc_final: 0.6575 (pt0) REVERT: A 331 ASP cc_start: 0.7304 (m-30) cc_final: 0.7004 (m-30) REVERT: A 332 GLU cc_start: 0.8010 (tp30) cc_final: 0.7702 (mp0) REVERT: A 420 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8501 (ptmt) REVERT: A 422 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7894 (tt) REVERT: B 121 HIS cc_start: 0.6194 (m90) cc_final: 0.5875 (m-70) REVERT: B 171 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7856 (ttpp) REVERT: B 268 ARG cc_start: 0.6587 (tpt170) cc_final: 0.6307 (tpt-90) REVERT: B 294 ARG cc_start: 0.7171 (mmp80) cc_final: 0.6694 (mpt180) REVERT: C 112 LEU cc_start: 0.0846 (tp) cc_final: 0.0323 (mm) REVERT: D 325 THR cc_start: 0.7209 (p) cc_final: 0.6992 (p) REVERT: D 354 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8634 (t) REVERT: E 34 GLU cc_start: 0.8452 (tt0) cc_final: 0.8206 (tt0) REVERT: E 65 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7582 (mm-30) REVERT: E 172 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8480 (t) REVERT: E 269 ARG cc_start: 0.8275 (ptp90) cc_final: 0.8048 (mtm180) REVERT: E 333 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7836 (ptp90) REVERT: E 335 GLU cc_start: 0.8443 (tt0) cc_final: 0.8235 (mt-10) REVERT: F 34 GLU cc_start: 0.8087 (tt0) cc_final: 0.7756 (mt-10) REVERT: F 143 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8774 (p) REVERT: F 188 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7575 (pm20) REVERT: F 301 VAL cc_start: 0.9068 (t) cc_final: 0.8826 (t) REVERT: G 91 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: G 206 LYS cc_start: 0.8407 (ptpp) cc_final: 0.8092 (mtpp) REVERT: H 139 GLN cc_start: 0.8621 (tp40) cc_final: 0.8352 (tp-100) REVERT: H 185 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7810 (ttm-80) REVERT: H 186 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: H 214 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8779 (tt) REVERT: H 304 TYR cc_start: 0.8387 (m-80) cc_final: 0.8179 (m-80) REVERT: H 318 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7387 (ptmm) REVERT: H 335 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: I 78 THR cc_start: 0.8069 (m) cc_final: 0.7807 (p) REVERT: I 113 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8462 (ttt-90) REVERT: I 133 TYR cc_start: 0.8046 (t80) cc_final: 0.7796 (t80) REVERT: I 155 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8026 (ttp-110) REVERT: I 203 ARG cc_start: 0.7291 (ptp-110) cc_final: 0.6745 (mtp-110) REVERT: I 324 TYR cc_start: 0.8112 (m-10) cc_final: 0.7815 (m-10) REVERT: J 124 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8212 (p) REVERT: J 194 ASN cc_start: 0.8524 (t160) cc_final: 0.8269 (t0) REVERT: J 220 ASP cc_start: 0.8784 (t0) cc_final: 0.8547 (t70) REVERT: K 37 MET cc_start: 0.6881 (ptm) cc_final: 0.5627 (ppp) REVERT: K 54 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5884 (tm-30) REVERT: K 61 GLU cc_start: 0.8540 (pt0) cc_final: 0.8192 (pp20) REVERT: K 134 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: K 155 ASP cc_start: 0.6569 (p0) cc_final: 0.4599 (p0) REVERT: K 157 GLU cc_start: 0.8051 (mp0) cc_final: 0.7309 (pm20) REVERT: K 173 GLU cc_start: 0.6790 (tp30) cc_final: 0.6478 (mm-30) REVERT: K 209 LYS cc_start: 0.8269 (tppt) cc_final: 0.7906 (tppp) outliers start: 85 outliers final: 28 residues processed: 386 average time/residue: 0.5757 time to fit residues: 261.4880 Evaluate side-chains 349 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 58 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 ASN D 170 ASN E 146 ASN F 129 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN H 310 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN I 341 GLN J 216 HIS ** K 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.145953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093933 restraints weight = 44277.071| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.49 r_work: 0.3108 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.8393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28649 Z= 0.163 Angle : 0.651 12.783 39386 Z= 0.334 Chirality : 0.043 0.339 4432 Planarity : 0.004 0.045 4823 Dihedral : 13.637 178.230 4808 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.80 % Allowed : 24.85 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3322 helix: 1.08 (0.15), residues: 1077 sheet: 0.50 (0.21), residues: 587 loop : -1.31 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 299 TYR 0.023 0.002 TYR D 324 PHE 0.033 0.002 PHE A 291 TRP 0.036 0.001 TRP B 247 HIS 0.005 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (28649) covalent geometry : angle 0.65150 / 0.33 (39386) hydrogen bonds : bond 0.03249 / 2.26 ( 1176) hydrogen bonds : angle 4.72366 / 3.34 ( 3238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 310 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6562 (tppt) cc_final: 0.6239 (tppt) REVERT: A 102 ASP cc_start: 0.8027 (p0) cc_final: 0.7655 (p0) REVERT: A 220 GLU cc_start: 0.8534 (tt0) cc_final: 0.7959 (tm-30) REVERT: A 223 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.7246 (p) REVERT: A 235 TYR cc_start: 0.8109 (m-80) cc_final: 0.7896 (m-80) REVERT: A 242 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8394 (mmmt) REVERT: A 281 MET cc_start: 0.6343 (tpt) cc_final: 0.6097 (mmp) REVERT: A 283 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.8094 (t-90) REVERT: A 306 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7091 (ttp80) REVERT: A 307 PHE cc_start: 0.7692 (m-80) cc_final: 0.7298 (m-10) REVERT: A 321 ARG cc_start: 0.7295 (tpm170) cc_final: 0.6596 (tpm-80) REVERT: A 324 GLN cc_start: 0.7038 (pt0) cc_final: 0.6584 (pt0) REVERT: A 331 ASP cc_start: 0.7478 (m-30) cc_final: 0.7122 (m-30) REVERT: A 332 GLU cc_start: 0.8302 (tp30) cc_final: 0.8062 (mm-30) REVERT: A 396 ASN cc_start: 0.7326 (m110) cc_final: 0.7118 (m110) REVERT: A 420 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8540 (ptmt) REVERT: A 422 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7977 (tt) REVERT: A 427 GLU cc_start: 0.7489 (tp30) cc_final: 0.7086 (tm-30) REVERT: B 106 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: B 121 HIS cc_start: 0.6302 (m90) cc_final: 0.5984 (m-70) REVERT: B 132 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: B 171 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8044 (ttpp) REVERT: B 294 ARG cc_start: 0.7225 (mmp80) cc_final: 0.6765 (mpt180) REVERT: C 112 LEU cc_start: 0.0740 (tp) cc_final: 0.0241 (mm) REVERT: D 354 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8757 (t) REVERT: E 34 GLU cc_start: 0.8446 (tt0) cc_final: 0.8200 (tt0) REVERT: E 65 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 172 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8558 (t) REVERT: E 269 ARG cc_start: 0.8268 (ptp90) cc_final: 0.8049 (mtm180) REVERT: E 333 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7941 (ptp90) REVERT: F 34 GLU cc_start: 0.8097 (tt0) cc_final: 0.7797 (mt-10) REVERT: F 143 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8800 (p) REVERT: F 188 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7616 (pm20) REVERT: F 335 GLU cc_start: 0.8433 (tt0) cc_final: 0.8176 (mt-10) REVERT: G 91 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: G 206 LYS cc_start: 0.8454 (ptpp) cc_final: 0.8208 (mtpp) REVERT: G 335 GLU cc_start: 0.8436 (tt0) cc_final: 0.8096 (pt0) REVERT: H 185 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7738 (ttm-80) REVERT: H 186 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: H 214 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8826 (tt) REVERT: H 335 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: I 79 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8089 (ptpp) REVERT: I 155 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8196 (ttp80) REVERT: I 203 ARG cc_start: 0.7369 (ptp-110) cc_final: 0.6907 (mtp-110) REVERT: I 318 LYS cc_start: 0.8594 (ptpt) cc_final: 0.8387 (ptpp) REVERT: I 324 TYR cc_start: 0.8387 (m-10) cc_final: 0.8144 (m-10) REVERT: J 124 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8240 (p) REVERT: J 173 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7787 (mp0) REVERT: J 187 LEU cc_start: 0.8528 (tt) cc_final: 0.8297 (tp) REVERT: J 208 GLN cc_start: 0.8170 (mt0) cc_final: 0.7953 (mt0) REVERT: J 220 ASP cc_start: 0.8982 (t0) cc_final: 0.8718 (t70) REVERT: K 37 MET cc_start: 0.7135 (ptm) cc_final: 0.5994 (ppp) REVERT: K 54 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6025 (tm-30) REVERT: K 61 GLU cc_start: 0.8616 (pt0) cc_final: 0.8250 (pp20) REVERT: K 134 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: K 173 GLU cc_start: 0.7018 (tp30) cc_final: 0.6620 (mm-30) REVERT: K 209 LYS cc_start: 0.8277 (tppt) cc_final: 0.7895 (tppp) outliers start: 73 outliers final: 34 residues processed: 360 average time/residue: 0.5734 time to fit residues: 242.5670 Evaluate side-chains 330 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 45 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 185 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 84 optimal weight: 40.0000 chunk 270 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 ASN D 170 ASN D 281 ASN E 102 ASN E 146 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.146540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093926 restraints weight = 51424.916| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.69 r_work: 0.3079 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.8634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28649 Z= 0.136 Angle : 0.634 12.945 39386 Z= 0.324 Chirality : 0.042 0.340 4432 Planarity : 0.004 0.042 4823 Dihedral : 13.619 177.875 4808 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.45 % Allowed : 25.15 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3322 helix: 1.18 (0.16), residues: 1077 sheet: 0.50 (0.21), residues: 587 loop : -1.29 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 52 TYR 0.016 0.001 TYR K 198 PHE 0.019 0.001 PHE A 287 TRP 0.033 0.001 TRP B 247 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (28649) covalent geometry : angle 0.63406 / 0.32 (39386) hydrogen bonds : bond 0.03147 / 2.19 ( 1176) hydrogen bonds : angle 4.68923 / 3.32 ( 3238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.8552 (tt0) cc_final: 0.7998 (tm-30) REVERT: A 223 SER cc_start: 0.7684 (t) cc_final: 0.7302 (p) REVERT: A 235 TYR cc_start: 0.8157 (m-80) cc_final: 0.7939 (m-80) REVERT: A 242 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8429 (mmmt) REVERT: A 283 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.8197 (t-90) REVERT: A 306 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7239 (ttp80) REVERT: A 321 ARG cc_start: 0.7318 (tpm170) cc_final: 0.6692 (tpm-80) REVERT: A 324 GLN cc_start: 0.7092 (pt0) cc_final: 0.6672 (pt0) REVERT: A 331 ASP cc_start: 0.7445 (m-30) cc_final: 0.7071 (m-30) REVERT: A 422 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8069 (tt) REVERT: B 121 HIS cc_start: 0.6305 (m90) cc_final: 0.5951 (m-70) REVERT: B 171 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8060 (ttpp) REVERT: B 268 ARG cc_start: 0.6594 (tpt170) cc_final: 0.6346 (tpt-90) REVERT: B 294 ARG cc_start: 0.7256 (mmp80) cc_final: 0.6790 (mpt180) REVERT: C 112 LEU cc_start: 0.1068 (tp) cc_final: 0.0607 (mm) REVERT: D 138 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7610 (mm) REVERT: D 354 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8776 (t) REVERT: E 34 GLU cc_start: 0.8456 (tt0) cc_final: 0.8247 (tt0) REVERT: E 65 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7564 (mm-30) REVERT: E 172 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8578 (t) REVERT: E 269 ARG cc_start: 0.8336 (ptp90) cc_final: 0.8082 (mtm-85) REVERT: E 333 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7962 (ptp90) REVERT: F 34 GLU cc_start: 0.8070 (tt0) cc_final: 0.7799 (mt-10) REVERT: F 143 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8842 (p) REVERT: F 188 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7656 (pm20) REVERT: F 335 GLU cc_start: 0.8471 (tt0) cc_final: 0.8203 (mt-10) REVERT: G 92 SER cc_start: 0.8069 (m) cc_final: 0.7817 (p) REVERT: G 206 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8244 (mtpp) REVERT: G 335 GLU cc_start: 0.8396 (tt0) cc_final: 0.8092 (pt0) REVERT: H 185 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7768 (ttm-80) REVERT: H 186 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: H 249 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8962 (mm-30) REVERT: H 335 GLU cc_start: 0.8400 (pm20) cc_final: 0.8089 (pm20) REVERT: I 78 THR cc_start: 0.8500 (m) cc_final: 0.8263 (p) REVERT: I 79 LYS cc_start: 0.8673 (ptmt) cc_final: 0.8143 (ptpp) REVERT: I 203 ARG cc_start: 0.7364 (ptp-110) cc_final: 0.6499 (mtp85) REVERT: I 318 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8378 (ptpp) REVERT: I 324 TYR cc_start: 0.8543 (m-10) cc_final: 0.8306 (m-10) REVERT: J 124 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8318 (p) REVERT: J 173 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7953 (mp0) REVERT: J 187 LEU cc_start: 0.8560 (tt) cc_final: 0.8342 (tp) REVERT: J 220 ASP cc_start: 0.8944 (t0) cc_final: 0.8610 (t70) REVERT: K 52 ARG cc_start: 0.8293 (ptm-80) cc_final: 0.8034 (ptp-170) REVERT: K 53 ASP cc_start: 0.8875 (m-30) cc_final: 0.8273 (m-30) REVERT: K 54 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6036 (tm-30) REVERT: K 61 GLU cc_start: 0.8622 (pt0) cc_final: 0.8260 (pp20) REVERT: K 134 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: K 155 ASP cc_start: 0.6560 (p0) cc_final: 0.6026 (p0) REVERT: K 157 GLU cc_start: 0.7784 (mp0) cc_final: 0.7028 (pm20) REVERT: K 173 GLU cc_start: 0.7026 (tp30) cc_final: 0.6646 (mm-30) outliers start: 64 outliers final: 37 residues processed: 335 average time/residue: 0.5416 time to fit residues: 212.9596 Evaluate side-chains 328 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 17 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 157 optimal weight: 0.0050 chunk 139 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 ASN D 170 ASN E 146 ASN G 91 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.146774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094104 restraints weight = 53486.054| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.74 r_work: 0.3100 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.8734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28649 Z= 0.132 Angle : 0.630 13.210 39386 Z= 0.322 Chirality : 0.042 0.345 4432 Planarity : 0.004 0.044 4823 Dihedral : 13.606 177.786 4808 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.26 % Allowed : 25.46 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3322 helix: 1.18 (0.16), residues: 1077 sheet: 0.50 (0.21), residues: 587 loop : -1.27 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 52 TYR 0.012 0.001 TYR J 128 PHE 0.022 0.001 PHE A 425 TRP 0.033 0.001 TRP B 247 HIS 0.006 0.001 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (28649) covalent geometry : angle 0.62975 / 0.32 (39386) hydrogen bonds : bond 0.03107 / 2.16 ( 1176) hydrogen bonds : angle 4.68180 / 3.31 ( 3238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 295 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8070 (pp20) REVERT: A 223 SER cc_start: 0.7690 (t) cc_final: 0.7301 (p) REVERT: A 235 TYR cc_start: 0.8183 (m-80) cc_final: 0.7965 (m-80) REVERT: A 242 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8429 (mmmt) REVERT: A 283 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8205 (t-90) REVERT: A 321 ARG cc_start: 0.7429 (tpm170) cc_final: 0.6910 (tpm-80) REVERT: A 324 GLN cc_start: 0.7058 (pt0) cc_final: 0.6637 (pt0) REVERT: A 331 ASP cc_start: 0.7457 (m-30) cc_final: 0.7152 (m-30) REVERT: A 422 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8154 (tt) REVERT: B 121 HIS cc_start: 0.6257 (m90) cc_final: 0.5872 (m-70) REVERT: B 171 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8091 (ttpp) REVERT: B 268 ARG cc_start: 0.6573 (tpt170) cc_final: 0.6326 (tpt-90) REVERT: B 294 ARG cc_start: 0.7198 (mmp80) cc_final: 0.6751 (mpt180) REVERT: C 112 LEU cc_start: 0.0890 (tp) cc_final: 0.0416 (mm) REVERT: D 138 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 354 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8799 (t) REVERT: E 34 GLU cc_start: 0.8458 (tt0) cc_final: 0.8244 (tt0) REVERT: E 37 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8312 (mp) REVERT: E 65 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7559 (mm-30) REVERT: E 172 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8579 (t) REVERT: E 269 ARG cc_start: 0.8326 (ptp90) cc_final: 0.8091 (mtm-85) REVERT: E 333 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7934 (ptp90) REVERT: F 34 GLU cc_start: 0.8092 (tt0) cc_final: 0.7825 (mt-10) REVERT: F 143 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8770 (p) REVERT: F 188 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7741 (pm20) REVERT: F 335 GLU cc_start: 0.8451 (tt0) cc_final: 0.8203 (mt-10) REVERT: G 92 SER cc_start: 0.8133 (m) cc_final: 0.7883 (p) REVERT: G 206 LYS cc_start: 0.8504 (ptpp) cc_final: 0.8282 (mtpp) REVERT: G 335 GLU cc_start: 0.8360 (tt0) cc_final: 0.8051 (pt0) REVERT: H 185 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7778 (ttm-80) REVERT: H 186 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: H 249 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8967 (mm-30) REVERT: I 79 LYS cc_start: 0.8740 (ptmt) cc_final: 0.8205 (ptpp) REVERT: I 203 ARG cc_start: 0.7473 (ptp-110) cc_final: 0.6563 (mtp85) REVERT: I 296 LEU cc_start: 0.8705 (mp) cc_final: 0.8154 (mp) REVERT: I 318 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8395 (ptpp) REVERT: I 324 TYR cc_start: 0.8593 (m-10) cc_final: 0.8366 (m-10) REVERT: J 124 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8321 (p) REVERT: J 150 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8895 (pt0) REVERT: J 173 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7919 (mp0) REVERT: J 220 ASP cc_start: 0.8976 (t0) cc_final: 0.8642 (t70) REVERT: K 37 MET cc_start: 0.7054 (ppp) cc_final: 0.6380 (ppp) REVERT: K 52 ARG cc_start: 0.8300 (ptm-80) cc_final: 0.7978 (ptp-170) REVERT: K 53 ASP cc_start: 0.8876 (m-30) cc_final: 0.7938 (m-30) REVERT: K 54 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: K 61 GLU cc_start: 0.8638 (pt0) cc_final: 0.8294 (pp20) REVERT: K 134 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8028 (tm-30) REVERT: K 155 ASP cc_start: 0.6536 (p0) cc_final: 0.6029 (p0) REVERT: K 157 GLU cc_start: 0.7778 (mp0) cc_final: 0.7037 (pm20) REVERT: K 173 GLU cc_start: 0.7055 (tp30) cc_final: 0.6682 (mm-30) REVERT: K 218 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8681 (tp) outliers start: 59 outliers final: 36 residues processed: 331 average time/residue: 0.5440 time to fit residues: 212.0478 Evaluate side-chains 333 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 CYS Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 310 optimal weight: 0.1980 chunk 124 optimal weight: 0.0470 chunk 45 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 168 optimal weight: 0.0770 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 240 GLN B 282 ASN D 170 ASN E 146 ASN F 129 ASN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096321 restraints weight = 47267.899| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.59 r_work: 0.3153 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.8880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28649 Z= 0.118 Angle : 0.628 13.323 39386 Z= 0.319 Chirality : 0.041 0.341 4432 Planarity : 0.004 0.042 4823 Dihedral : 13.570 177.356 4808 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.19 % Allowed : 25.96 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3322 helix: 1.23 (0.16), residues: 1077 sheet: 0.45 (0.21), residues: 592 loop : -1.23 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 52 TYR 0.030 0.002 TYR A 336 PHE 0.046 0.001 PHE A 425 TRP 0.031 0.001 TRP B 247 HIS 0.004 0.001 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (28649) covalent geometry : angle 0.62818 / 0.32 (39386) hydrogen bonds : bond 0.03056 / 2.10 ( 1176) hydrogen bonds : angle 4.62956 / 3.28 ( 3238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11808.38 seconds wall clock time: 201 minutes 1.23 seconds (12061.23 seconds total)