Starting phenix.real_space_refine on Fri Mar 6 04:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tax_25789/03_2026/7tax_25789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tax_25789/03_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_25789/03_2026/7tax_25789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tax_25789/03_2026/7tax_25789.map" model { file = "/net/cci-nas-00/data/ceres_data/7tax_25789/03_2026/7tax_25789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tax_25789/03_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-5986/lib/python3.9/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: 14 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: 6.12, per 1000 atoms: 0.22 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.15 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: 5.24 Time building geometry restraints manager: 3.09 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: 38820 2.34 - 4.68: 501 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: 16614 35.90 - 71.81: 474 71.81 - 107.71: 45 107.71 - 143.62: 1 143.62 - 179.52: 5 Dihedral angle restraints: 17139 sinusoidal: 7493 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 17136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3645 0.051 - 0.103: 635 0.103 - 0.154: 140 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.590 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 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= 0.173 Angle : 0.668 11.694 39386 Z= 0.369 Chirality : 0.042 0.257 4432 Planarity : 0.005 0.077 4823 Dihedral : 16.218 179.523 10913 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 covalent geometry : bond 0.00311 (28649) covalent geometry : angle 0.66807 (39386) hydrogen bonds : bond 0.18486 ( 1176) hydrogen bonds : angle 7.24627 ( 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 : 1.011 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: 0.5599 time to fit residues: 573.0854 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 : 0.947 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 129 ASN A 177 GLN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 255 ASN A 328 GLN A 416 GLN B 18 GLN B 21 ASN B 82 ASN B 89 ASN B 104 HIS B 168 GLN B 282 ASN B 293 HIS C 19 GLN D 170 ASN D 281 ASN D 343 HIS F 186 GLN F 242 GLN G 160 ASN G 163 ASN G 260 GLN G 281 ASN H 96 GLN H 242 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN I 281 ASN J 26 HIS J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.151873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102688 restraints weight = 45885.542| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.54 r_work: 0.3257 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28649 Z= 0.243 Angle : 0.836 10.891 39386 Z= 0.432 Chirality : 0.048 0.253 4432 Planarity : 0.006 0.087 4823 Dihedral : 16.391 179.722 5034 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.52 % Allowed : 15.34 % Favored : 80.14 % 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: -0.71 (0.14), residues: 3322 helix: 0.26 (0.15), residues: 1052 sheet: 0.71 (0.21), residues: 529 loop : -1.33 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 191 TYR 0.030 0.003 TYR F 324 PHE 0.029 0.003 PHE A 16 TRP 0.029 0.003 TRP H 193 HIS 0.013 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00545 (28649) covalent geometry : angle 0.83629 (39386) hydrogen bonds : bond 0.04472 ( 1176) hydrogen bonds : angle 5.29178 ( 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 653 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 535 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.6858 (tppp) cc_final: 0.6543 (tppp) REVERT: A 102 ASP cc_start: 0.7866 (p0) cc_final: 0.7644 (p0) REVERT: A 281 MET cc_start: 0.5733 (tpt) cc_final: 0.5442 (tpt) REVERT: A 283 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.8230 (t-90) REVERT: A 296 GLU cc_start: 0.7791 (tp30) cc_final: 0.7386 (tp30) REVERT: A 299 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8001 (ttp80) REVERT: A 300 LEU cc_start: 0.8438 (mm) cc_final: 0.7571 (mt) REVERT: A 329 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6962 (mp) REVERT: B 27 LEU cc_start: 0.8333 (mt) cc_final: 0.8119 (mt) REVERT: B 72 GLN cc_start: 0.8292 (pt0) cc_final: 0.7717 (tt0) REVERT: B 106 GLU cc_start: 0.7454 (tt0) cc_final: 0.7245 (tm-30) REVERT: B 197 LEU cc_start: 0.8176 (tp) cc_final: 0.7885 (tm) REVERT: B 218 ARG cc_start: 0.7133 (ptt180) cc_final: 0.6584 (ptt180) REVERT: B 282 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8369 (t0) REVERT: C 112 LEU cc_start: 0.0933 (tp) cc_final: 0.0565 (mm) REVERT: D 354 VAL cc_start: 0.8500 (t) cc_final: 0.8288 (t) REVERT: E 65 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7855 (mm-30) REVERT: E 143 THR cc_start: 0.8699 (t) cc_final: 0.8442 (p) REVERT: F 80 ASP cc_start: 0.8866 (t0) cc_final: 0.8605 (t0) REVERT: F 139 GLN cc_start: 0.8593 (tp40) cc_final: 0.7986 (tt0) REVERT: F 143 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8589 (p) REVERT: F 188 GLU cc_start: 0.7730 (mt-10) cc_final: 0.6919 (pm20) REVERT: F 318 LYS cc_start: 0.8311 (ptmm) cc_final: 0.6625 (mmtp) REVERT: F 320 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7810 (mmtt) REVERT: G 238 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8101 (tt) REVERT: G 269 ARG cc_start: 0.7401 (ttm170) cc_final: 0.7173 (mtp180) REVERT: H 38 ASP cc_start: 0.8816 (t0) cc_final: 0.8591 (t0) REVERT: H 74 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8656 (m-40) REVERT: H 99 ASP cc_start: 0.8740 (m-30) cc_final: 0.8526 (t0) REVERT: H 139 GLN cc_start: 0.8072 (tp40) cc_final: 0.7817 (tp40) REVERT: H 143 THR cc_start: 0.8694 (t) cc_final: 0.8328 (p) REVERT: H 185 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7541 (ttm-80) REVERT: H 186 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7516 (mp10) REVERT: H 254 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8085 (tptm) REVERT: H 335 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: I 113 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7817 (ttt-90) REVERT: I 136 LYS cc_start: 0.8720 (tptm) cc_final: 0.8080 (tptp) REVERT: I 203 ARG cc_start: 0.6564 (ptp-110) cc_final: 0.6282 (mtp-110) REVERT: I 320 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8135 (mmmm) REVERT: I 324 TYR cc_start: 0.7171 (m-10) cc_final: 0.6895 (m-10) REVERT: J 37 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: J 81 ASP cc_start: 0.6521 (t0) cc_final: 0.6256 (t0) REVERT: J 134 GLU cc_start: 0.8257 (pp20) cc_final: 0.7941 (pp20) REVERT: J 155 ASP cc_start: 0.6932 (t0) cc_final: 0.6680 (p0) REVERT: J 158 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7259 (mm-30) REVERT: K 36 GLU cc_start: 0.7564 (tt0) cc_final: 0.7284 (tt0) REVERT: K 61 GLU cc_start: 0.8253 (pt0) cc_final: 0.7902 (pp20) REVERT: K 127 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8376 (pt0) REVERT: K 134 GLU cc_start: 0.7572 (tm-30) cc_final: 0.6821 (tp30) REVERT: K 173 GLU cc_start: 0.6684 (tp30) cc_final: 0.6403 (mm-30) REVERT: K 209 LYS cc_start: 0.8038 (tppt) cc_final: 0.7624 (tppp) outliers start: 118 outliers final: 24 residues processed: 620 average time/residue: 0.5959 time to fit residues: 436.2209 Evaluate side-chains 405 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 371 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 214 LEU 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 48 SER Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 151 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 59 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 218 optimal weight: 0.9980 chunk 304 optimal weight: 6.9990 chunk 242 optimal weight: 0.3980 chunk 210 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 186 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 83 HIS ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 82 ASN D 170 ASN D 183 HIS D 281 ASN E 102 ASN E 146 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS G 96 GLN G 260 GLN G 348 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN I 96 GLN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS K 25 HIS ** K 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099399 restraints weight = 54426.130| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.75 r_work: 0.3164 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28649 Z= 0.139 Angle : 0.620 10.669 39386 Z= 0.316 Chirality : 0.043 0.479 4432 Planarity : 0.004 0.048 4823 Dihedral : 15.928 178.778 5024 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.87 % Allowed : 19.79 % Favored : 76.34 % 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: -0.33 (0.14), residues: 3322 helix: 0.89 (0.15), residues: 1060 sheet: 0.78 (0.21), residues: 538 loop : -1.29 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 64 TYR 0.015 0.002 TYR D 324 PHE 0.045 0.002 PHE A 20 TRP 0.022 0.001 TRP A 155 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00315 (28649) covalent geometry : angle 0.62026 (39386) hydrogen bonds : bond 0.03531 ( 1176) hydrogen bonds : angle 4.83275 ( 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 507 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 406 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.6721 (tppp) cc_final: 0.6510 (tppt) REVERT: A 102 ASP cc_start: 0.7767 (p0) cc_final: 0.7516 (p0) REVERT: A 123 LEU cc_start: 0.5392 (mm) cc_final: 0.4228 (tp) REVERT: A 220 GLU cc_start: 0.8350 (tt0) cc_final: 0.7774 (tm-30) REVERT: A 281 MET cc_start: 0.5738 (tpt) cc_final: 0.5169 (tpt) REVERT: A 283 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8114 (t-90) REVERT: A 296 GLU cc_start: 0.7884 (tp30) cc_final: 0.7215 (tp30) REVERT: A 299 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7977 (ttp80) REVERT: A 300 LEU cc_start: 0.8180 (mm) cc_final: 0.7284 (mt) REVERT: A 321 ARG cc_start: 0.7264 (tpm170) cc_final: 0.6554 (tpm-80) REVERT: A 324 GLN cc_start: 0.7002 (pt0) cc_final: 0.6773 (pm20) REVERT: A 397 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7326 (mtm180) REVERT: A 420 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8422 (ptmt) REVERT: A 427 GLU cc_start: 0.7146 (tp30) cc_final: 0.6939 (tp30) REVERT: B 72 GLN cc_start: 0.8270 (pt0) cc_final: 0.7882 (tt0) REVERT: B 106 GLU cc_start: 0.7540 (tt0) cc_final: 0.7208 (tm-30) REVERT: B 121 HIS cc_start: 0.6122 (m-70) cc_final: 0.5693 (m-70) REVERT: B 171 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7651 (ttpp) REVERT: C 112 LEU cc_start: 0.0881 (tp) cc_final: 0.0438 (mm) REVERT: C 117 MET cc_start: 0.1517 (OUTLIER) cc_final: 0.1222 (mpp) REVERT: D 159 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7547 (m-70) REVERT: D 312 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7557 (pttp) REVERT: D 354 VAL cc_start: 0.8570 (t) cc_final: 0.8339 (t) REVERT: E 34 GLU cc_start: 0.8391 (tt0) cc_final: 0.8118 (tt0) REVERT: E 65 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7466 (mm-30) REVERT: E 203 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8030 (mmm160) REVERT: F 65 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8100 (mm-30) REVERT: F 80 ASP cc_start: 0.8809 (t0) cc_final: 0.8507 (t0) REVERT: F 85 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8620 (mtmm) REVERT: F 139 GLN cc_start: 0.8516 (tp40) cc_final: 0.8021 (tt0) REVERT: F 143 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8611 (p) REVERT: F 188 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7185 (pm20) REVERT: F 318 LYS cc_start: 0.8488 (ptmm) cc_final: 0.6954 (mmtt) REVERT: G 65 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8323 (mt-10) REVERT: G 96 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: G 319 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6278 (pt0) REVERT: H 139 GLN cc_start: 0.8175 (tp40) cc_final: 0.7895 (tp40) REVERT: H 185 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7494 (ttm-80) REVERT: H 203 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7079 (mmm160) REVERT: H 335 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: I 79 LYS cc_start: 0.8468 (ptmm) cc_final: 0.8114 (pmmt) REVERT: I 113 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8024 (ttt-90) REVERT: I 136 LYS cc_start: 0.8643 (tptm) cc_final: 0.8356 (tptp) REVERT: I 203 ARG cc_start: 0.6617 (ptp-110) cc_final: 0.6330 (mtp-110) REVERT: I 206 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7334 (mtmm) REVERT: I 320 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8090 (mmmm) REVERT: J 54 GLU cc_start: 0.8467 (tp30) cc_final: 0.8175 (tm-30) REVERT: J 73 ASP cc_start: 0.7152 (p0) cc_final: 0.6840 (p0) REVERT: J 150 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: J 158 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7532 (mm-30) REVERT: K 54 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: K 61 GLU cc_start: 0.8261 (pt0) cc_final: 0.7919 (pp20) REVERT: K 73 ASP cc_start: 0.7388 (m-30) cc_final: 0.6983 (m-30) REVERT: K 127 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8075 (pt0) REVERT: K 155 ASP cc_start: 0.5537 (p0) cc_final: 0.4529 (p0) REVERT: K 209 LYS cc_start: 0.8139 (tppt) cc_final: 0.7749 (tppp) outliers start: 101 outliers final: 25 residues processed: 463 average time/residue: 0.6137 time to fit residues: 334.0918 Evaluate side-chains 375 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 319 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain J residue 152 LEU 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 151 VAL Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 309 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 256 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 324 GLN B 282 ASN B 293 HIS D 170 ASN E 102 ASN E 146 ASN E 348 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN G 343 HIS ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN I 96 GLN I 183 HIS I 242 GLN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 HIS J 27 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.145449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094906 restraints weight = 47295.895| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.74 r_work: 0.3062 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28649 Z= 0.172 Angle : 0.653 11.076 39386 Z= 0.332 Chirality : 0.044 0.644 4432 Planarity : 0.005 0.062 4823 Dihedral : 15.878 178.393 5024 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.91 % Allowed : 19.33 % Favored : 75.77 % 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: -0.34 (0.14), residues: 3322 helix: 0.92 (0.15), residues: 1067 sheet: 0.64 (0.21), residues: 566 loop : -1.32 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 269 TYR 0.023 0.002 TYR D 133 PHE 0.036 0.002 PHE A 425 TRP 0.028 0.002 TRP A 414 HIS 0.009 0.001 HIS K 5 Details of bonding type rmsd covalent geometry : bond 0.00397 (28649) covalent geometry : angle 0.65262 (39386) hydrogen bonds : bond 0.03532 ( 1176) hydrogen bonds : angle 4.78935 ( 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 484 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 356 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7147 (tppp) cc_final: 0.6750 (tppt) REVERT: A 220 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: A 235 TYR cc_start: 0.8202 (m-80) cc_final: 0.7915 (m-80) REVERT: A 281 MET cc_start: 0.6223 (tpt) cc_final: 0.5942 (mmp) REVERT: A 283 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8133 (t-90) REVERT: A 296 GLU cc_start: 0.8008 (tp30) cc_final: 0.7106 (tp30) REVERT: A 299 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8147 (ttp80) REVERT: A 300 LEU cc_start: 0.8237 (mm) cc_final: 0.7261 (mt) REVERT: A 329 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 397 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7592 (mtt180) REVERT: A 420 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8579 (ptmt) REVERT: A 427 GLU cc_start: 0.7709 (tp30) cc_final: 0.7441 (tp30) REVERT: B 72 GLN cc_start: 0.8568 (pt0) cc_final: 0.8337 (tt0) REVERT: B 132 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: B 171 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8044 (ttpp) REVERT: B 294 ARG cc_start: 0.7244 (mmp80) cc_final: 0.6827 (mpt180) REVERT: C 112 LEU cc_start: 0.0749 (tp) cc_final: 0.0329 (mm) REVERT: C 117 MET cc_start: 0.0984 (OUTLIER) cc_final: 0.0766 (mtt) REVERT: D 169 ARG cc_start: 0.8565 (ttt90) cc_final: 0.7980 (ttm-80) REVERT: D 354 VAL cc_start: 0.8896 (t) cc_final: 0.8628 (t) REVERT: E 37 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8348 (mp) REVERT: E 64 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8254 (mtm-85) REVERT: E 65 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 172 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8562 (t) REVERT: E 203 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8495 (mmm160) REVERT: E 216 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8371 (mm-30) REVERT: E 335 GLU cc_start: 0.8410 (tt0) cc_final: 0.8189 (mt-10) REVERT: F 34 GLU cc_start: 0.8108 (tt0) cc_final: 0.7769 (mt-10) REVERT: F 65 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8459 (mm-30) REVERT: F 79 LYS cc_start: 0.9218 (tmmt) cc_final: 0.8986 (ptpt) REVERT: F 81 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8672 (mmm-85) REVERT: F 139 GLN cc_start: 0.8859 (tp40) cc_final: 0.8336 (tt0) REVERT: F 143 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8814 (p) REVERT: F 188 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7654 (pm20) REVERT: F 318 LYS cc_start: 0.8995 (ptmm) cc_final: 0.7719 (mmtm) REVERT: F 335 GLU cc_start: 0.8464 (tt0) cc_final: 0.8142 (mt-10) REVERT: G 65 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8703 (mt-10) REVERT: G 203 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7758 (mmm-85) REVERT: G 206 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8133 (mtpp) REVERT: H 185 ARG cc_start: 0.8384 (ttp80) cc_final: 0.7750 (ttm-80) REVERT: H 186 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: H 214 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8691 (tt) REVERT: H 249 GLU cc_start: 0.9274 (mm-30) cc_final: 0.9033 (mm-30) REVERT: H 318 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7457 (ptmm) REVERT: I 79 LYS cc_start: 0.8699 (ptmm) cc_final: 0.8216 (ptpp) REVERT: I 113 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8392 (ttt-90) REVERT: I 203 ARG cc_start: 0.7395 (ptp-110) cc_final: 0.7049 (mtp-110) REVERT: I 320 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8346 (mmmm) REVERT: I 324 TYR cc_start: 0.8269 (m-10) cc_final: 0.8026 (m-10) REVERT: J 53 ASP cc_start: 0.8190 (m-30) cc_final: 0.7988 (m-30) REVERT: J 158 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7924 (mm-30) REVERT: J 173 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8081 (mp0) REVERT: J 208 GLN cc_start: 0.8147 (mt0) cc_final: 0.7871 (mt0) REVERT: J 220 ASP cc_start: 0.8818 (t0) cc_final: 0.8533 (t70) REVERT: K 52 ARG cc_start: 0.8423 (ptm-80) cc_final: 0.7827 (mtt90) REVERT: K 53 ASP cc_start: 0.9149 (m-30) cc_final: 0.8769 (m-30) REVERT: K 54 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: K 61 GLU cc_start: 0.8480 (pt0) cc_final: 0.8117 (pp20) REVERT: K 73 ASP cc_start: 0.7777 (m-30) cc_final: 0.7384 (m-30) REVERT: K 134 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7306 (tp30) REVERT: K 209 LYS cc_start: 0.8282 (tppt) cc_final: 0.8047 (tppp) outliers start: 128 outliers final: 36 residues processed: 443 average time/residue: 0.6178 time to fit residues: 322.1425 Evaluate side-chains 336 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 117 MET 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 E residue 29 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR 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 118 VAL 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 252 LEU Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 151 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: 1.9990 chunk 3 optimal weight: 40.0000 chunk 260 optimal weight: 0.0980 chunk 157 optimal weight: 0.9990 chunk 85 optimal weight: 0.0570 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN D 170 ASN E 146 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN G 91 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.145761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095807 restraints weight = 44304.751| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.64 r_work: 0.3082 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.8752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28649 Z= 0.129 Angle : 0.591 9.703 39386 Z= 0.300 Chirality : 0.041 0.266 4432 Planarity : 0.004 0.044 4823 Dihedral : 15.784 177.803 5024 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 3.72 % Allowed : 21.43 % Favored : 74.85 % 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: -0.18 (0.14), residues: 3322 helix: 1.18 (0.15), residues: 1082 sheet: 0.71 (0.21), residues: 557 loop : -1.32 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 64 TYR 0.013 0.001 TYR D 324 PHE 0.028 0.001 PHE A 425 TRP 0.025 0.001 TRP A 414 HIS 0.006 0.001 HIS H 159 Details of bonding type rmsd covalent geometry : bond 0.00291 (28649) covalent geometry : angle 0.59094 (39386) hydrogen bonds : bond 0.03122 ( 1176) hydrogen bonds : angle 4.59361 ( 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 410 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 313 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.5879 (tm) REVERT: A 71 LYS cc_start: 0.7091 (tppp) cc_final: 0.6662 (tppt) REVERT: A 220 GLU cc_start: 0.8557 (tt0) cc_final: 0.7969 (pp20) REVERT: A 223 SER cc_start: 0.7748 (OUTLIER) cc_final: 0.7326 (p) REVERT: A 281 MET cc_start: 0.6486 (tpt) cc_final: 0.6172 (mmp) REVERT: A 283 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8170 (t-90) REVERT: A 290 ASP cc_start: 0.8639 (p0) cc_final: 0.8034 (p0) REVERT: A 296 GLU cc_start: 0.7971 (tp30) cc_final: 0.7165 (tp30) REVERT: A 299 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8274 (ttp80) REVERT: A 300 LEU cc_start: 0.8291 (mm) cc_final: 0.7750 (mt) REVERT: A 306 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7057 (ttp80) REVERT: A 331 ASP cc_start: 0.7132 (m-30) cc_final: 0.6883 (m-30) REVERT: A 420 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8446 (ptpp) REVERT: A 427 GLU cc_start: 0.7856 (tp30) cc_final: 0.7423 (tm-30) REVERT: B 132 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: B 171 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8126 (ttpp) REVERT: B 294 ARG cc_start: 0.7342 (mmp80) cc_final: 0.6889 (mpt180) REVERT: C 112 LEU cc_start: 0.0881 (tp) cc_final: 0.0419 (mm) REVERT: C 117 MET cc_start: 0.1170 (OUTLIER) cc_final: 0.0948 (mtt) REVERT: D 128 CYS cc_start: 0.7234 (p) cc_final: 0.7023 (t) REVERT: D 169 ARG cc_start: 0.8570 (ttt90) cc_final: 0.7960 (ttm-80) REVERT: D 170 ASN cc_start: 0.7966 (m-40) cc_final: 0.7713 (m110) REVERT: D 312 LYS cc_start: 0.7713 (ptmt) cc_final: 0.7471 (pttp) REVERT: D 324 TYR cc_start: 0.8188 (m-10) cc_final: 0.7954 (m-80) REVERT: D 354 VAL cc_start: 0.8993 (t) cc_final: 0.8731 (t) REVERT: E 37 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8374 (mp) REVERT: E 65 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7633 (mm-30) REVERT: E 172 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8609 (t) REVERT: E 203 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8425 (mmm160) REVERT: E 216 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8369 (mm-30) REVERT: E 333 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8084 (ptp90) REVERT: F 34 GLU cc_start: 0.8066 (tt0) cc_final: 0.7820 (mt-10) REVERT: F 65 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8568 (mm-30) REVERT: F 79 LYS cc_start: 0.9019 (tmmt) cc_final: 0.8779 (ptpt) REVERT: F 85 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8714 (mtmm) REVERT: F 139 GLN cc_start: 0.8924 (tp40) cc_final: 0.8460 (tt0) REVERT: F 143 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8773 (p) REVERT: F 188 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7684 (pm20) REVERT: F 318 LYS cc_start: 0.9038 (ptmm) cc_final: 0.7737 (mmtt) REVERT: F 335 GLU cc_start: 0.8376 (tt0) cc_final: 0.8128 (mt-10) REVERT: G 57 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: G 65 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8717 (mt-10) REVERT: G 94 ASN cc_start: 0.8475 (p0) cc_final: 0.8257 (p0) REVERT: G 96 GLN cc_start: 0.8951 (mt0) cc_final: 0.8590 (pm20) REVERT: G 206 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8312 (mtpp) REVERT: G 216 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8483 (mt-10) REVERT: G 242 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8919 (mm110) REVERT: H 185 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7877 (ttm-80) REVERT: H 186 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: H 249 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9005 (mm-30) REVERT: H 320 LYS cc_start: 0.8374 (mmmm) cc_final: 0.8108 (mmtp) REVERT: I 79 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8269 (ptpp) REVERT: I 113 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8492 (ttt-90) REVERT: J 158 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7993 (mm-30) REVERT: J 167 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8616 (mm) REVERT: J 173 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8002 (mp0) REVERT: K 52 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.7774 (mpt90) REVERT: K 53 ASP cc_start: 0.9074 (m-30) cc_final: 0.8783 (m-30) REVERT: K 54 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6105 (tm-30) REVERT: K 61 GLU cc_start: 0.8534 (pt0) cc_final: 0.8158 (pp20) REVERT: K 127 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8178 (pt0) REVERT: K 134 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7348 (tp30) REVERT: K 166 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: K 218 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8640 (tp) outliers start: 97 outliers final: 34 residues processed: 380 average time/residue: 0.6531 time to fit residues: 288.2285 Evaluate side-chains 330 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR 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 132 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 117 MET 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 E residue 29 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 216 GLU 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 128 CYS Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 37 MET 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 151 VAL Chi-restraints excluded: chain K residue 166 GLU 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: 0.6980 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 3 optimal weight: 40.0000 chunk 321 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 324 GLN B 194 GLN B 220 ASN B 282 ASN B 305 HIS D 348 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 248 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086666 restraints weight = 53449.139| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.94 r_work: 0.2917 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.9931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28649 Z= 0.216 Angle : 0.680 10.610 39386 Z= 0.347 Chirality : 0.044 0.272 4432 Planarity : 0.005 0.056 4823 Dihedral : 15.987 178.888 5024 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.33 % Allowed : 21.28 % Favored : 74.39 % 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: -0.26 (0.14), residues: 3322 helix: 0.99 (0.15), residues: 1081 sheet: 0.73 (0.21), residues: 508 loop : -1.24 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 64 TYR 0.024 0.002 TYR D 133 PHE 0.039 0.002 PHE A 291 TRP 0.044 0.002 TRP B 247 HIS 0.009 0.001 HIS H 159 Details of bonding type rmsd covalent geometry : bond 0.00492 (28649) covalent geometry : angle 0.68001 (39386) hydrogen bonds : bond 0.03710 ( 1176) hydrogen bonds : angle 4.86914 ( 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 434 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 321 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7791 (tppp) cc_final: 0.7435 (tppt) REVERT: A 220 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: A 223 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7546 (p) REVERT: A 283 HIS cc_start: 0.8691 (OUTLIER) cc_final: 0.8242 (t-90) REVERT: A 296 GLU cc_start: 0.7879 (tp30) cc_final: 0.7012 (tp30) REVERT: A 299 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8197 (ttp80) REVERT: A 300 LEU cc_start: 0.8457 (mm) cc_final: 0.7733 (mt) REVERT: A 325 LEU cc_start: 0.7720 (tp) cc_final: 0.7437 (tt) REVERT: A 329 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 331 ASP cc_start: 0.7407 (m-30) cc_final: 0.7025 (m-30) REVERT: A 332 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: A 343 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8040 (pp) REVERT: A 347 TRP cc_start: 0.8222 (p-90) cc_final: 0.7713 (p-90) REVERT: A 420 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8567 (ptpp) REVERT: A 427 GLU cc_start: 0.8168 (tp30) cc_final: 0.7684 (tm-30) REVERT: B 132 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: B 171 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8187 (ttpp) REVERT: B 294 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7203 (mmt180) REVERT: C 112 LEU cc_start: 0.0756 (tp) cc_final: 0.0266 (mm) REVERT: D 293 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6834 (tt0) REVERT: E 65 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7879 (mm-30) REVERT: E 95 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5960 (tp) REVERT: E 172 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8699 (t) REVERT: E 208 ASP cc_start: 0.7919 (t0) cc_final: 0.7679 (t0) REVERT: F 64 ARG cc_start: 0.8513 (ptt-90) cc_final: 0.8169 (ptt90) REVERT: F 139 GLN cc_start: 0.9013 (tp40) cc_final: 0.8595 (tt0) REVERT: F 143 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8922 (p) REVERT: F 188 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7883 (pm20) REVERT: F 318 LYS cc_start: 0.9321 (ptmm) cc_final: 0.8163 (mmtm) REVERT: F 335 GLU cc_start: 0.8629 (tt0) cc_final: 0.8407 (mt-10) REVERT: G 65 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8882 (mt-10) REVERT: G 92 SER cc_start: 0.8654 (m) cc_final: 0.8331 (p) REVERT: G 206 LYS cc_start: 0.8701 (ptpp) cc_final: 0.8446 (mtpp) REVERT: G 320 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8265 (mmmm) REVERT: G 324 TYR cc_start: 0.9180 (m-80) cc_final: 0.8754 (m-80) REVERT: G 335 GLU cc_start: 0.8424 (tt0) cc_final: 0.8124 (pt0) REVERT: H 56 GLN cc_start: 0.8738 (pm20) cc_final: 0.8496 (pm20) REVERT: H 74 ASN cc_start: 0.8721 (m110) cc_final: 0.8322 (p0) REVERT: H 134 ARG cc_start: 0.8386 (tmt170) cc_final: 0.8142 (ttt180) REVERT: H 185 ARG cc_start: 0.8383 (ttp80) cc_final: 0.7789 (ttm-80) REVERT: H 186 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8315 (mp10) REVERT: H 214 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8867 (tt) REVERT: I 44 MET cc_start: 0.9291 (ttm) cc_final: 0.9088 (mtp) REVERT: I 72 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8754 (pp) REVERT: I 79 LYS cc_start: 0.8941 (ptmm) cc_final: 0.8608 (ptpt) REVERT: I 113 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8623 (ttt-90) REVERT: I 135 ASP cc_start: 0.9106 (m-30) cc_final: 0.8777 (m-30) REVERT: J 53 ASP cc_start: 0.8458 (m-30) cc_final: 0.8258 (m-30) REVERT: J 81 ASP cc_start: 0.8238 (t70) cc_final: 0.7802 (t0) REVERT: J 167 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8763 (mt) REVERT: J 220 ASP cc_start: 0.9220 (t0) cc_final: 0.8886 (t70) REVERT: K 54 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: K 61 GLU cc_start: 0.8530 (pt0) cc_final: 0.8219 (pp20) REVERT: K 62 PHE cc_start: 0.8626 (t80) cc_final: 0.8204 (t80) REVERT: K 127 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8198 (pt0) REVERT: K 134 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: K 155 ASP cc_start: 0.7050 (p0) cc_final: 0.6470 (p0) REVERT: K 158 GLU cc_start: 0.7976 (pt0) cc_final: 0.7671 (pm20) REVERT: K 166 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: K 173 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7111 (mm-30) REVERT: K 194 ASN cc_start: 0.8300 (t0) cc_final: 0.7955 (t0) outliers start: 113 outliers final: 36 residues processed: 402 average time/residue: 0.6464 time to fit residues: 302.2548 Evaluate side-chains 317 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 313 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 E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 97 THR 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 186 GLN Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU 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 166 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 196 optimal weight: 0.9990 chunk 230 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 324 GLN B 220 ASN B 282 ASN D 170 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.089581 restraints weight = 53636.332| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.68 r_work: 0.2988 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 1.0042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28649 Z= 0.128 Angle : 0.597 10.955 39386 Z= 0.302 Chirality : 0.041 0.237 4432 Planarity : 0.004 0.050 4823 Dihedral : 15.812 177.942 5024 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.99 % Allowed : 22.85 % Favored : 74.16 % 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: -0.10 (0.14), residues: 3322 helix: 1.24 (0.16), residues: 1083 sheet: 0.70 (0.21), residues: 532 loop : -1.22 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 64 TYR 0.024 0.001 TYR D 133 PHE 0.023 0.001 PHE A 425 TRP 0.028 0.001 TRP A 414 HIS 0.005 0.001 HIS D 159 Details of bonding type rmsd covalent geometry : bond 0.00286 (28649) covalent geometry : angle 0.59720 (39386) hydrogen bonds : bond 0.03096 ( 1176) hydrogen bonds : angle 4.63999 ( 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 389 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 311 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7569 (tppp) cc_final: 0.7241 (tppt) REVERT: A 220 GLU cc_start: 0.8620 (tt0) cc_final: 0.8030 (pp20) REVERT: A 223 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7552 (p) REVERT: A 283 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8318 (t-90) REVERT: A 296 GLU cc_start: 0.7911 (tp30) cc_final: 0.6938 (tp30) REVERT: A 299 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8255 (ttp80) REVERT: A 300 LEU cc_start: 0.8415 (mm) cc_final: 0.7780 (mt) REVERT: A 306 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7270 (ttp80) REVERT: A 331 ASP cc_start: 0.7289 (m-30) cc_final: 0.6981 (m-30) REVERT: A 332 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: A 343 LEU cc_start: 0.8119 (pt) cc_final: 0.7833 (pt) REVERT: A 347 TRP cc_start: 0.8324 (p-90) cc_final: 0.7725 (p-90) REVERT: A 420 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8478 (ptpp) REVERT: A 421 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 424 MET cc_start: 0.8442 (mtp) cc_final: 0.8114 (mtp) REVERT: B 132 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: B 171 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8128 (ttpp) REVERT: B 294 ARG cc_start: 0.7642 (mmp80) cc_final: 0.7249 (mmt180) REVERT: C 112 LEU cc_start: 0.0869 (tp) cc_final: 0.0353 (mm) REVERT: D 169 ARG cc_start: 0.8605 (ttt90) cc_final: 0.8220 (ttm-80) REVERT: E 65 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7863 (mm-30) REVERT: E 153 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8300 (mt) REVERT: E 172 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8698 (t) REVERT: E 188 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 64 ARG cc_start: 0.8550 (ptt-90) cc_final: 0.8274 (ptt90) REVERT: F 85 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8855 (mtmm) REVERT: F 139 GLN cc_start: 0.9005 (tp40) cc_final: 0.8643 (tt0) REVERT: F 188 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7893 (pm20) REVERT: F 318 LYS cc_start: 0.9272 (ptmm) cc_final: 0.8100 (mmtm) REVERT: G 92 SER cc_start: 0.8309 (m) cc_final: 0.7989 (p) REVERT: G 206 LYS cc_start: 0.8681 (ptpp) cc_final: 0.8458 (mtpp) REVERT: G 242 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8947 (mm110) REVERT: G 324 TYR cc_start: 0.9122 (m-80) cc_final: 0.8816 (m-80) REVERT: G 335 GLU cc_start: 0.8284 (tt0) cc_final: 0.7983 (pt0) REVERT: H 56 GLN cc_start: 0.8721 (pm20) cc_final: 0.8478 (pm20) REVERT: H 74 ASN cc_start: 0.8649 (m110) cc_final: 0.8336 (p0) REVERT: H 185 ARG cc_start: 0.8429 (ttp80) cc_final: 0.7873 (ttm-80) REVERT: H 186 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: I 72 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8741 (pp) REVERT: I 79 LYS cc_start: 0.8933 (ptmm) cc_final: 0.8509 (ptpp) REVERT: I 113 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8572 (ttt-90) REVERT: I 135 ASP cc_start: 0.9083 (m-30) cc_final: 0.8740 (m-30) REVERT: J 54 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8730 (tp30) REVERT: J 157 GLU cc_start: 0.8677 (mp0) cc_final: 0.8334 (mp0) REVERT: J 167 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8686 (mt) REVERT: J 173 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8101 (mp0) REVERT: K 52 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.8215 (mtt90) REVERT: K 54 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: K 61 GLU cc_start: 0.8551 (pt0) cc_final: 0.8220 (pp20) REVERT: K 62 PHE cc_start: 0.8619 (t80) cc_final: 0.8218 (t80) REVERT: K 127 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8164 (pt0) REVERT: K 134 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: K 155 ASP cc_start: 0.7078 (p0) cc_final: 0.6283 (p0) REVERT: K 158 GLU cc_start: 0.7809 (pt0) cc_final: 0.7589 (pm20) REVERT: K 173 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7251 (mm-30) REVERT: K 209 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8138 (ttpt) REVERT: K 225 LYS cc_start: 0.8797 (tmtm) cc_final: 0.8532 (tttp) outliers start: 78 outliers final: 25 residues processed: 363 average time/residue: 0.6442 time to fit residues: 272.0142 Evaluate side-chains 306 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 188 GLU 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 312 LYS 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 186 GLN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 58 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 306 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 393 ASN B 64 HIS B 220 ASN B 282 ASN D 170 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.090217 restraints weight = 44235.501| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.44 r_work: 0.3015 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 1.0196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28649 Z= 0.134 Angle : 0.594 10.890 39386 Z= 0.302 Chirality : 0.041 0.219 4432 Planarity : 0.004 0.049 4823 Dihedral : 15.774 177.567 5024 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.03 % Allowed : 22.78 % Favored : 74.19 % 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: -0.01 (0.14), residues: 3322 helix: 1.34 (0.16), residues: 1083 sheet: 0.69 (0.21), residues: 546 loop : -1.18 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 64 TYR 0.025 0.001 TYR D 133 PHE 0.020 0.001 PHE A 291 TRP 0.030 0.001 TRP A 414 HIS 0.005 0.001 HIS H 159 Details of bonding type rmsd covalent geometry : bond 0.00303 (28649) covalent geometry : angle 0.59436 (39386) hydrogen bonds : bond 0.03081 ( 1176) hydrogen bonds : angle 4.56588 ( 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 365 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 286 time to evaluate : 0.939 Fit side-chains REVERT: A 71 LYS cc_start: 0.7649 (tppp) cc_final: 0.7339 (tppp) REVERT: A 220 GLU cc_start: 0.8620 (tt0) cc_final: 0.8035 (pp20) REVERT: A 223 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7621 (p) REVERT: A 283 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8298 (t-90) REVERT: A 296 GLU cc_start: 0.7993 (tp30) cc_final: 0.7069 (tp30) REVERT: A 299 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8257 (ttp80) REVERT: A 300 LEU cc_start: 0.8498 (mm) cc_final: 0.7890 (mt) REVERT: A 306 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7234 (ttp80) REVERT: A 324 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: A 331 ASP cc_start: 0.7449 (m-30) cc_final: 0.7017 (m-30) REVERT: A 332 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: A 347 TRP cc_start: 0.8379 (p-90) cc_final: 0.7825 (p-90) REVERT: A 420 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8505 (ptpp) REVERT: A 424 MET cc_start: 0.8460 (mtp) cc_final: 0.8118 (mtp) REVERT: B 132 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: B 171 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8105 (ttpp) REVERT: B 288 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: B 294 ARG cc_start: 0.7792 (mmp80) cc_final: 0.7414 (mmt180) REVERT: C 80 ARG cc_start: 0.7623 (mpt-90) cc_final: 0.7092 (ptp90) REVERT: C 112 LEU cc_start: 0.0836 (tp) cc_final: 0.0329 (mm) REVERT: D 169 ARG cc_start: 0.8563 (ttt90) cc_final: 0.8156 (ttm-80) REVERT: D 170 ASN cc_start: 0.8113 (m-40) cc_final: 0.7785 (m110) REVERT: D 182 ASN cc_start: 0.8182 (m-40) cc_final: 0.7819 (m-40) REVERT: D 354 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8990 (t) REVERT: E 65 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7710 (mm-30) REVERT: E 188 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: F 188 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7866 (pm20) REVERT: F 318 LYS cc_start: 0.9291 (ptmm) cc_final: 0.8095 (mmtt) REVERT: G 65 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8769 (mm-30) REVERT: G 242 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8959 (mm110) REVERT: G 324 TYR cc_start: 0.9107 (m-80) cc_final: 0.8822 (m-80) REVERT: G 335 GLU cc_start: 0.8238 (tt0) cc_final: 0.7952 (pt0) REVERT: G 351 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.7829 (ttt90) REVERT: H 74 ASN cc_start: 0.8590 (m110) cc_final: 0.8366 (p0) REVERT: H 185 ARG cc_start: 0.8397 (ttp80) cc_final: 0.7864 (ttm-80) REVERT: H 186 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: I 44 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.9013 (mtp) REVERT: I 72 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8757 (pp) REVERT: I 79 LYS cc_start: 0.8983 (ptmm) cc_final: 0.8558 (ptpp) REVERT: I 113 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8656 (ttt-90) REVERT: I 135 ASP cc_start: 0.9090 (m-30) cc_final: 0.8761 (m-30) REVERT: I 138 LEU cc_start: 0.9048 (tm) cc_final: 0.8802 (mm) REVERT: J 167 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8661 (mt) REVERT: J 173 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8049 (mp0) REVERT: J 206 ASN cc_start: 0.8808 (m110) cc_final: 0.8389 (m-40) REVERT: K 54 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: K 61 GLU cc_start: 0.8565 (pt0) cc_final: 0.8251 (pp20) REVERT: K 62 PHE cc_start: 0.8551 (t80) cc_final: 0.8205 (t80) REVERT: K 127 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8183 (pt0) REVERT: K 134 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: K 155 ASP cc_start: 0.7034 (p0) cc_final: 0.6316 (p0) REVERT: K 157 GLU cc_start: 0.7313 (pm20) cc_final: 0.7112 (pm20) REVERT: K 173 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7237 (mm-30) REVERT: K 209 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8193 (ttpt) REVERT: K 225 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8550 (tttm) outliers start: 79 outliers final: 33 residues processed: 338 average time/residue: 0.6654 time to fit residues: 261.0312 Evaluate side-chains 311 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP 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 29 SER Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 351 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 186 GLN Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU 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 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 225 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 45 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 185 optimal weight: 0.0020 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 0.0040 chunk 181 optimal weight: 0.0060 chunk 84 optimal weight: 9.9990 chunk 270 optimal weight: 0.8980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN B 220 ASN B 282 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 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 = 0.3900 r_free = 0.3900 target = 0.144613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092686 restraints weight = 51748.452| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.68 r_work: 0.3041 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 1.0261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28649 Z= 0.110 Angle : 0.595 11.342 39386 Z= 0.299 Chirality : 0.040 0.214 4432 Planarity : 0.004 0.047 4823 Dihedral : 15.700 176.853 5024 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.38 % Allowed : 23.85 % Favored : 73.77 % 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: 0.06 (0.14), residues: 3322 helix: 1.46 (0.16), residues: 1084 sheet: 0.75 (0.21), residues: 571 loop : -1.22 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 170 TYR 0.024 0.001 TYR D 133 PHE 0.019 0.001 PHE A 20 TRP 0.033 0.001 TRP A 414 HIS 0.006 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00245 (28649) covalent geometry : angle 0.59464 (39386) hydrogen bonds : bond 0.02935 ( 1176) hydrogen bonds : angle 4.47788 ( 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 349 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7446 (tppp) cc_final: 0.7016 (tppt) REVERT: A 220 GLU cc_start: 0.8597 (tt0) cc_final: 0.7957 (pp20) REVERT: A 223 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7626 (p) REVERT: A 283 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8400 (t70) REVERT: A 290 ASP cc_start: 0.8411 (p0) cc_final: 0.8180 (p0) REVERT: A 296 GLU cc_start: 0.7961 (tp30) cc_final: 0.6792 (tp30) REVERT: A 299 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8250 (ttp80) REVERT: A 300 LEU cc_start: 0.8494 (mm) cc_final: 0.7666 (mt) REVERT: A 306 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7205 (ttp80) REVERT: A 331 ASP cc_start: 0.7364 (m-30) cc_final: 0.6922 (m-30) REVERT: A 332 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: A 347 TRP cc_start: 0.8326 (p-90) cc_final: 0.7709 (p-90) REVERT: A 420 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8536 (ptpp) REVERT: A 424 MET cc_start: 0.8482 (mtp) cc_final: 0.8131 (mtp) REVERT: B 132 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: B 171 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8003 (ttpp) REVERT: B 288 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: B 294 ARG cc_start: 0.7802 (mmp80) cc_final: 0.7366 (mmt180) REVERT: C 80 ARG cc_start: 0.7615 (mpt-90) cc_final: 0.7132 (ptp90) REVERT: C 112 LEU cc_start: 0.0763 (tp) cc_final: 0.0267 (mm) REVERT: D 159 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7502 (m-70) REVERT: D 278 LYS cc_start: 0.7999 (tttp) cc_final: 0.7768 (mttm) REVERT: D 354 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.9022 (t) REVERT: E 65 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7658 (mm-30) REVERT: E 188 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: E 189 VAL cc_start: 0.9099 (m) cc_final: 0.8899 (t) REVERT: E 206 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8694 (mptt) REVERT: F 87 ASP cc_start: 0.8827 (m-30) cc_final: 0.8570 (m-30) REVERT: F 135 ASP cc_start: 0.9023 (m-30) cc_final: 0.8725 (m-30) REVERT: F 188 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7824 (pm20) REVERT: F 318 LYS cc_start: 0.9246 (ptmm) cc_final: 0.8067 (mmtm) REVERT: G 94 ASN cc_start: 0.8677 (m110) cc_final: 0.8420 (m-40) REVERT: G 242 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8984 (mm110) REVERT: G 335 GLU cc_start: 0.8197 (tt0) cc_final: 0.7917 (pt0) REVERT: G 351 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.7749 (ttt90) REVERT: H 56 GLN cc_start: 0.8693 (pm20) cc_final: 0.8191 (pm20) REVERT: H 74 ASN cc_start: 0.8578 (m110) cc_final: 0.8341 (p0) REVERT: H 102 ASN cc_start: 0.8710 (p0) cc_final: 0.8497 (p0) REVERT: H 185 ARG cc_start: 0.8363 (ttp80) cc_final: 0.7837 (ttm-80) REVERT: H 208 ASP cc_start: 0.8376 (t0) cc_final: 0.8143 (t0) REVERT: I 44 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8980 (mtp) REVERT: I 72 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8763 (pp) REVERT: I 79 LYS cc_start: 0.8978 (ptmm) cc_final: 0.8539 (ptpp) REVERT: I 135 ASP cc_start: 0.9127 (m-30) cc_final: 0.8797 (m-30) REVERT: I 138 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8841 (mm) REVERT: J 167 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8562 (mt) REVERT: J 173 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8022 (mp0) REVERT: J 206 ASN cc_start: 0.8789 (m110) cc_final: 0.8367 (m-40) REVERT: K 54 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: K 61 GLU cc_start: 0.8570 (pt0) cc_final: 0.8272 (pp20) REVERT: K 62 PHE cc_start: 0.8478 (t80) cc_final: 0.8197 (t80) REVERT: K 76 GLU cc_start: 0.7288 (mp0) cc_final: 0.6983 (mp0) REVERT: K 127 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8154 (pt0) REVERT: K 134 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: K 155 ASP cc_start: 0.7466 (p0) cc_final: 0.6933 (p0) outliers start: 62 outliers final: 23 residues processed: 327 average time/residue: 0.6701 time to fit residues: 253.9602 Evaluate side-chains 304 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 134 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 17 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 231 optimal weight: 2.9990 chunk 155 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN B 121 HIS B 220 ASN B 282 ASN D 170 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS K 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091748 restraints weight = 53909.188| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.72 r_work: 0.3024 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 1.0375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28649 Z= 0.119 Angle : 0.607 11.652 39386 Z= 0.303 Chirality : 0.040 0.232 4432 Planarity : 0.004 0.048 4823 Dihedral : 15.707 177.140 5024 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.92 % Allowed : 24.62 % Favored : 73.47 % 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: 0.08 (0.14), residues: 3322 helix: 1.47 (0.16), residues: 1088 sheet: 0.73 (0.21), residues: 567 loop : -1.20 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 64 TYR 0.023 0.001 TYR D 133 PHE 0.029 0.001 PHE A 425 TRP 0.036 0.001 TRP A 414 HIS 0.006 0.001 HIS D 159 Details of bonding type rmsd covalent geometry : bond 0.00267 (28649) covalent geometry : angle 0.60677 (39386) hydrogen bonds : bond 0.02974 ( 1176) hydrogen bonds : angle 4.45911 ( 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 328 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7503 (tppp) cc_final: 0.7076 (tppt) REVERT: A 220 GLU cc_start: 0.8596 (tt0) cc_final: 0.7945 (pp20) REVERT: A 223 SER cc_start: 0.8131 (OUTLIER) cc_final: 0.7722 (p) REVERT: A 283 HIS cc_start: 0.8749 (OUTLIER) cc_final: 0.8385 (t-90) REVERT: A 296 GLU cc_start: 0.7938 (tp30) cc_final: 0.6776 (tp30) REVERT: A 299 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8226 (ttp80) REVERT: A 300 LEU cc_start: 0.8497 (mm) cc_final: 0.7679 (mt) REVERT: A 306 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7440 (ttp80) REVERT: A 307 PHE cc_start: 0.8088 (m-10) cc_final: 0.7657 (m-80) REVERT: A 320 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8614 (mt0) REVERT: A 324 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: A 331 ASP cc_start: 0.7409 (m-30) cc_final: 0.6918 (m-30) REVERT: A 332 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7087 (tp30) REVERT: A 347 TRP cc_start: 0.8331 (p-90) cc_final: 0.7766 (p-90) REVERT: A 424 MET cc_start: 0.8524 (mtp) cc_final: 0.8099 (mtp) REVERT: B 132 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: B 171 LYS cc_start: 0.8252 (mtpp) cc_final: 0.8002 (ttpp) REVERT: B 268 ARG cc_start: 0.6721 (ttt90) cc_final: 0.6463 (tpt-90) REVERT: B 288 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: B 294 ARG cc_start: 0.7811 (mmp80) cc_final: 0.7399 (mmt180) REVERT: C 80 ARG cc_start: 0.7587 (mpt-90) cc_final: 0.7143 (ptp90) REVERT: C 112 LEU cc_start: 0.0777 (tp) cc_final: 0.0297 (mm) REVERT: D 170 ASN cc_start: 0.8256 (m-40) cc_final: 0.7909 (m-40) REVERT: D 243 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6649 (pp20) REVERT: D 278 LYS cc_start: 0.7946 (tttp) cc_final: 0.7705 (mttm) REVERT: D 354 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.9039 (t) REVERT: E 65 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7649 (mm-30) REVERT: E 188 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: E 189 VAL cc_start: 0.9123 (m) cc_final: 0.8920 (t) REVERT: E 206 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8585 (mppt) REVERT: E 333 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8129 (ptp90) REVERT: F 87 ASP cc_start: 0.8825 (m-30) cc_final: 0.8577 (m-30) REVERT: F 135 ASP cc_start: 0.9009 (m-30) cc_final: 0.8722 (m-30) REVERT: F 188 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7841 (pm20) REVERT: F 318 LYS cc_start: 0.9249 (ptmm) cc_final: 0.8106 (mmtt) REVERT: G 94 ASN cc_start: 0.8713 (m110) cc_final: 0.8453 (m-40) REVERT: G 242 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8978 (mm110) REVERT: G 335 GLU cc_start: 0.8222 (tt0) cc_final: 0.7954 (pt0) REVERT: G 351 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.7790 (ttt90) REVERT: H 74 ASN cc_start: 0.8590 (m110) cc_final: 0.8360 (p0) REVERT: H 102 ASN cc_start: 0.8701 (p0) cc_final: 0.8475 (p0) REVERT: H 185 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7850 (ttm-80) REVERT: H 208 ASP cc_start: 0.8370 (t0) cc_final: 0.8124 (t0) REVERT: I 44 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.9020 (mtp) REVERT: I 72 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8779 (pp) REVERT: I 79 LYS cc_start: 0.8956 (ptmm) cc_final: 0.8514 (ptpp) REVERT: I 135 ASP cc_start: 0.9120 (m-30) cc_final: 0.8780 (m-30) REVERT: I 138 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8840 (mm) REVERT: J 65 ASP cc_start: 0.8976 (t0) cc_final: 0.8676 (t0) REVERT: J 167 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8536 (mt) REVERT: J 173 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7991 (mp0) REVERT: J 206 ASN cc_start: 0.8797 (m110) cc_final: 0.8304 (m-40) REVERT: K 37 MET cc_start: 0.7533 (mpp) cc_final: 0.7243 (ptm) REVERT: K 54 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: K 61 GLU cc_start: 0.8597 (pt0) cc_final: 0.8278 (pp20) REVERT: K 62 PHE cc_start: 0.8432 (t80) cc_final: 0.8166 (t80) REVERT: K 127 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8156 (pt0) REVERT: K 134 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: K 209 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8087 (ttpt) outliers start: 50 outliers final: 23 residues processed: 312 average time/residue: 0.6382 time to fit residues: 232.6471 Evaluate side-chains 311 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 195 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 310 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 324 GLN B 121 HIS B 220 ASN B 282 ASN E 129 ASN E 348 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS K 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087454 restraints weight = 47360.060| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.91 r_work: 0.2939 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 1.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28649 Z= 0.195 Angle : 0.662 11.487 39386 Z= 0.333 Chirality : 0.043 0.300 4432 Planarity : 0.004 0.050 4823 Dihedral : 15.830 177.843 5024 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.99 % Allowed : 24.81 % Favored : 73.20 % 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: -0.02 (0.14), residues: 3322 helix: 1.30 (0.16), residues: 1083 sheet: 0.78 (0.21), residues: 532 loop : -1.18 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 64 TYR 0.024 0.002 TYR D 133 PHE 0.041 0.002 PHE A 425 TRP 0.055 0.002 TRP B 247 HIS 0.008 0.001 HIS H 159 Details of bonding type rmsd covalent geometry : bond 0.00448 (28649) covalent geometry : angle 0.66229 (39386) hydrogen bonds : bond 0.03338 ( 1176) hydrogen bonds : angle 4.64481 ( 3238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12837.12 seconds wall clock time: 217 minutes 58.98 seconds (13078.98 seconds total)