Starting phenix.real_space_refine on Fri Mar 15 10:38:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfo_0879/03_2024/6lfo_0879_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfo_0879/03_2024/6lfo_0879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfo_0879/03_2024/6lfo_0879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfo_0879/03_2024/6lfo_0879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfo_0879/03_2024/6lfo_0879_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfo_0879/03_2024/6lfo_0879_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.033 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 1821 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6128 2.51 5 N 1632 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "R GLU 42": "OE1" <-> "OE2" Residue "R GLU 127": "OE1" <-> "OE2" Residue "R GLU 198": "OE1" <-> "OE2" Residue "S TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9573 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 525 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "R" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2451 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.04, per 1000 atoms: 0.63 Number of scatterers: 9573 At special positions: 0 Unit cell: (87.36, 122.027, 155.307, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1745 8.00 N 1632 7.00 C 6128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 34 " distance=2.01 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 50 " distance=2.04 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.04 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 15 sheets defined 32.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.678A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.614A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.562A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 4.398A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 277' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.662A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.634A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 23 removed outlier: 3.987A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.769A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.526A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.675A pdb=" N VAL D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 45 No H-bonds generated for 'chain 'R' and resid 43 through 45' Processing helix chain 'R' and resid 48 through 74 removed outlier: 3.756A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 4.223A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Proline residue: R 102 - end of helix removed outlier: 3.892A pdb=" N VAL R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 135 removed outlier: 3.595A pdb=" N ASN R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR R 131 " --> pdb=" O GLU R 127 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE R 134 " --> pdb=" O PHE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 146 removed outlier: 3.546A pdb=" N SER R 141 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 160 Processing helix chain 'R' and resid 162 through 183 removed outlier: 3.520A pdb=" N LEU R 175 " --> pdb=" O GLY R 171 " (cutoff:3.500A) Proline residue: R 179 - end of helix removed outlier: 3.743A pdb=" N PHE R 183 " --> pdb=" O PRO R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 218 removed outlier: 3.949A pdb=" N LEU R 210 " --> pdb=" O ASN R 206 " (cutoff:3.500A) Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 221 through 228 Processing helix chain 'R' and resid 231 through 240 removed outlier: 3.540A pdb=" N PHE R 239 " --> pdb=" O LEU R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 263 removed outlier: 3.934A pdb=" N ARG R 251 " --> pdb=" O HIS R 247 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 279 removed outlier: 3.533A pdb=" N VAL R 270 " --> pdb=" O PRO R 266 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU R 272 " --> pdb=" O ASN R 268 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR R 275 " --> pdb=" O LEU R 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 304 removed outlier: 4.170A pdb=" N ALA R 298 " --> pdb=" O ARG R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 314 Processing helix chain 'R' and resid 319 through 331 removed outlier: 4.117A pdb=" N LEU R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS R 327 " --> pdb=" O HIS R 323 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 320 through 323 removed outlier: 3.764A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.900A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.753A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.611A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.525A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 296 through 298 removed outlier: 3.586A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.624A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 48 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.379A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.844A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 26 through 28 removed outlier: 4.128A pdb=" N ILE D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.923A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 144 through 148 Processing sheet with id= N, first strand: chain 'S' and resid 162 through 164 Processing sheet with id= O, first strand: chain 'S' and resid 213 through 215 removed outlier: 3.827A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2964 1.33 - 1.46: 2130 1.46 - 1.58: 4581 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9771 Sorted by residual: bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.89e+00 bond pdb=" CB VAL S 97 " pdb=" CG2 VAL S 97 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.28e+00 bond pdb=" CB TRP S 47 " pdb=" CG TRP S 47 " ideal model delta sigma weight residual 1.498 1.416 0.082 3.10e-02 1.04e+03 7.01e+00 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.421 0.092 3.90e-02 6.57e+02 5.55e+00 bond pdb=" CG LEU B 168 " pdb=" CD1 LEU B 168 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.77: 138 104.77 - 112.10: 4774 112.10 - 119.43: 3463 119.43 - 126.76: 4740 126.76 - 134.09: 133 Bond angle restraints: 13248 Sorted by residual: angle pdb=" CA MET A 240 " pdb=" CB MET A 240 " pdb=" CG MET A 240 " ideal model delta sigma weight residual 114.10 124.54 -10.44 2.00e+00 2.50e-01 2.72e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" CA LEU R 44 " pdb=" CB LEU R 44 " pdb=" CG LEU R 44 " ideal model delta sigma weight residual 116.30 131.31 -15.01 3.50e+00 8.16e-02 1.84e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C SER R 190 " pdb=" N ASN R 191 " pdb=" CA ASN R 191 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5171 17.97 - 35.93: 591 35.93 - 53.90: 90 53.90 - 71.86: 15 71.86 - 89.83: 8 Dihedral angle restraints: 5875 sinusoidal: 2309 harmonic: 3566 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 -134.87 -45.13 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CB CYS D 7 " pdb=" SG CYS D 7 " pdb=" SG CYS D 34 " pdb=" CB CYS D 34 " ideal model delta sinusoidal sigma weight residual -86.00 -143.72 57.72 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.03 -54.03 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 5872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1113 0.064 - 0.128: 356 0.128 - 0.192: 49 0.192 - 0.257: 11 0.257 - 0.321: 2 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CB ILE S 100 " pdb=" CA ILE S 100 " pdb=" CG1 ILE S 100 " pdb=" CG2 ILE S 100 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB THR A 181 " pdb=" CA THR A 181 " pdb=" OG1 THR A 181 " pdb=" CG2 THR A 181 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA MET A 240 " pdb=" N MET A 240 " pdb=" C MET A 240 " pdb=" CB MET A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1528 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 30 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO R 31 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR S 178 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C TYR S 178 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR S 178 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG S 179 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 112 " -0.029 2.00e-02 2.50e+03 1.61e-02 6.44e+00 pdb=" CG TRP R 112 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP R 112 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP R 112 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 112 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 112 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP R 112 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 112 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 112 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 112 " 0.003 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2650 2.78 - 3.31: 8404 3.31 - 3.84: 15671 3.84 - 4.37: 18081 4.37 - 4.90: 31234 Nonbonded interactions: 76040 Sorted by model distance: nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.255 2.440 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 228 " model vdw 2.267 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.299 2.440 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.305 2.520 nonbonded pdb=" OG SER S 149 " pdb=" N SER S 150 " model vdw 2.308 2.520 ... (remaining 76035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.070 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.860 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.013 0.116 9771 Z= 0.837 Angle : 1.133 15.015 13248 Z= 0.594 Chirality : 0.062 0.321 1531 Planarity : 0.007 0.107 1660 Dihedral : 15.003 89.828 3553 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.29 % Allowed : 11.96 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.54 (0.17), residues: 1212 helix: -4.48 (0.11), residues: 387 sheet: -3.37 (0.26), residues: 270 loop : -3.08 (0.21), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP R 112 HIS 0.010 0.002 HIS B 91 PHE 0.023 0.003 PHE B 235 TYR 0.033 0.003 TYR S 178 ARG 0.011 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 306 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7603 (mtm110) REVERT: A 35 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8457 (mttm) REVERT: A 232 LEU cc_start: 0.8521 (tt) cc_final: 0.7534 (tt) REVERT: A 243 MET cc_start: 0.8964 (tpp) cc_final: 0.8726 (mmm) REVERT: A 341 ASP cc_start: 0.7813 (t70) cc_final: 0.7427 (t0) REVERT: B 15 LYS cc_start: 0.9199 (tptt) cc_final: 0.8691 (ttmm) REVERT: B 157 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8615 (tt) REVERT: B 188 MET cc_start: 0.8492 (mmm) cc_final: 0.7976 (mpp) REVERT: B 209 LYS cc_start: 0.8812 (mttm) cc_final: 0.8527 (mttt) REVERT: B 210 LEU cc_start: 0.9183 (tp) cc_final: 0.8927 (tt) REVERT: B 223 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7556 (p) REVERT: B 339 TRP cc_start: 0.8429 (m100) cc_final: 0.8143 (m100) REVERT: R 55 TYR cc_start: 0.8706 (m-80) cc_final: 0.8175 (m-80) REVERT: R 63 LEU cc_start: 0.7965 (mm) cc_final: 0.7567 (mm) REVERT: R 90 LEU cc_start: 0.8649 (tp) cc_final: 0.8381 (tp) REVERT: R 103 ILE cc_start: 0.7650 (mp) cc_final: 0.7443 (mp) REVERT: R 131 TYR cc_start: 0.7500 (m-80) cc_final: 0.7289 (m-10) REVERT: R 134 ILE cc_start: 0.8190 (mm) cc_final: 0.7933 (mm) REVERT: R 145 TYR cc_start: 0.8994 (t80) cc_final: 0.8756 (t80) REVERT: R 209 MET cc_start: 0.7637 (mmm) cc_final: 0.6987 (mmm) REVERT: R 227 MET cc_start: 0.7959 (mtp) cc_final: 0.7710 (mtp) REVERT: S 3 GLN cc_start: 0.7864 (pt0) cc_final: 0.7545 (pt0) REVERT: S 13 GLN cc_start: 0.8432 (mm110) cc_final: 0.7988 (pp30) REVERT: S 68 PHE cc_start: 0.8922 (m-10) cc_final: 0.8552 (m-10) REVERT: S 219 GLN cc_start: 0.8968 (pp30) cc_final: 0.8562 (pp30) outliers start: 3 outliers final: 0 residues processed: 309 average time/residue: 0.2701 time to fit residues: 108.3315 Evaluate side-chains 225 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 204 GLN A 213 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 220 GLN B 340 ASN D 8 GLN R 66 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 ASN R 310 ASN R 332 HIS S 39 GLN S 167 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9771 Z= 0.180 Angle : 0.626 8.478 13248 Z= 0.321 Chirality : 0.041 0.163 1531 Planarity : 0.005 0.090 1660 Dihedral : 5.847 38.469 1395 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.02 % Allowed : 18.87 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.20), residues: 1212 helix: -2.79 (0.20), residues: 388 sheet: -2.85 (0.28), residues: 269 loop : -2.67 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 112 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE S 227 TYR 0.023 0.001 TYR S 178 ARG 0.010 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7410 (mtm110) REVERT: A 35 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8293 (mttm) REVERT: A 232 LEU cc_start: 0.8798 (tt) cc_final: 0.8549 (tp) REVERT: A 296 TYR cc_start: 0.8514 (t80) cc_final: 0.8230 (t80) REVERT: A 304 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 310 LEU cc_start: 0.8979 (mt) cc_final: 0.8573 (mt) REVERT: B 9 GLN cc_start: 0.8163 (mm110) cc_final: 0.7803 (mp10) REVERT: B 15 LYS cc_start: 0.9148 (tptt) cc_final: 0.8824 (mtpp) REVERT: B 17 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 129 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7519 (mmp-170) REVERT: B 134 ARG cc_start: 0.8269 (ptt-90) cc_final: 0.7804 (ptt-90) REVERT: B 209 LYS cc_start: 0.8724 (mttm) cc_final: 0.8373 (mttt) REVERT: B 292 PHE cc_start: 0.7972 (m-10) cc_final: 0.7639 (m-80) REVERT: B 339 TRP cc_start: 0.8340 (m100) cc_final: 0.8126 (m100) REVERT: C 38 MET cc_start: 0.8334 (ttp) cc_final: 0.8108 (ttp) REVERT: C 47 GLU cc_start: 0.7565 (mp0) cc_final: 0.7076 (mp0) REVERT: R 55 TYR cc_start: 0.8608 (m-80) cc_final: 0.8353 (m-80) REVERT: R 63 LEU cc_start: 0.7936 (mm) cc_final: 0.7497 (mm) REVERT: R 125 LEU cc_start: 0.8534 (tp) cc_final: 0.8284 (tp) REVERT: R 126 LYS cc_start: 0.7541 (ttmm) cc_final: 0.6881 (tppt) REVERT: R 209 MET cc_start: 0.7491 (mmm) cc_final: 0.6976 (mmm) REVERT: R 226 ILE cc_start: 0.8952 (tt) cc_final: 0.8607 (tt) REVERT: R 242 HIS cc_start: 0.7782 (p90) cc_final: 0.7551 (p-80) REVERT: S 3 GLN cc_start: 0.7941 (pt0) cc_final: 0.7665 (pt0) REVERT: S 20 LEU cc_start: 0.7796 (mt) cc_final: 0.7505 (mt) REVERT: S 47 TRP cc_start: 0.8254 (t60) cc_final: 0.8052 (t60) REVERT: S 219 GLN cc_start: 0.8922 (pp30) cc_final: 0.8440 (pp30) REVERT: S 232 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7909 (ttpp) outliers start: 31 outliers final: 14 residues processed: 296 average time/residue: 0.2269 time to fit residues: 91.5139 Evaluate side-chains 249 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 87 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN R 47 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9771 Z= 0.159 Angle : 0.588 8.291 13248 Z= 0.296 Chirality : 0.041 0.175 1531 Planarity : 0.004 0.088 1660 Dihedral : 5.153 37.192 1392 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.28 % Allowed : 20.53 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.22), residues: 1212 helix: -1.57 (0.24), residues: 384 sheet: -2.46 (0.29), residues: 265 loop : -2.33 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 112 HIS 0.002 0.001 HIS B 91 PHE 0.014 0.001 PHE R 130 TYR 0.019 0.001 TYR S 178 ARG 0.005 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 257 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8550 (m-30) cc_final: 0.8103 (t0) REVERT: A 32 ARG cc_start: 0.7708 (mtt-85) cc_final: 0.7491 (mtm110) REVERT: A 35 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8383 (mttm) REVERT: A 304 GLN cc_start: 0.8321 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 310 LEU cc_start: 0.9046 (mt) cc_final: 0.8649 (mt) REVERT: B 9 GLN cc_start: 0.8314 (mm110) cc_final: 0.8046 (mp10) REVERT: B 15 LYS cc_start: 0.9132 (tptt) cc_final: 0.8797 (mtpp) REVERT: B 17 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 129 ARG cc_start: 0.7760 (tpp-160) cc_final: 0.7373 (mmm160) REVERT: B 258 ASP cc_start: 0.6942 (t0) cc_final: 0.6741 (t0) REVERT: B 260 GLU cc_start: 0.8125 (tt0) cc_final: 0.7867 (tt0) REVERT: B 289 TYR cc_start: 0.8764 (m-80) cc_final: 0.8559 (m-80) REVERT: B 292 PHE cc_start: 0.7871 (m-10) cc_final: 0.7385 (m-80) REVERT: B 325 MET cc_start: 0.8268 (tpp) cc_final: 0.7966 (tpp) REVERT: C 27 ARG cc_start: 0.7635 (mtt90) cc_final: 0.6998 (mtt90) REVERT: D 24 GLU cc_start: 0.5125 (pp20) cc_final: 0.4846 (pp20) REVERT: R 63 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7528 (mm) REVERT: R 71 LEU cc_start: 0.8112 (tp) cc_final: 0.7727 (tp) REVERT: R 99 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8440 (mm) REVERT: R 127 GLU cc_start: 0.8262 (tp30) cc_final: 0.8036 (tp30) REVERT: R 137 LEU cc_start: 0.8136 (mp) cc_final: 0.7928 (mp) REVERT: R 209 MET cc_start: 0.7558 (mmm) cc_final: 0.7060 (mmm) REVERT: R 226 ILE cc_start: 0.8962 (tt) cc_final: 0.8623 (tt) REVERT: R 242 HIS cc_start: 0.7786 (p90) cc_final: 0.7583 (p-80) REVERT: S 3 GLN cc_start: 0.7821 (pt0) cc_final: 0.7570 (pt0) REVERT: S 91 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7783 (t) REVERT: S 219 GLN cc_start: 0.9081 (pp30) cc_final: 0.8442 (pp30) outliers start: 44 outliers final: 28 residues processed: 286 average time/residue: 0.2120 time to fit residues: 83.6871 Evaluate side-chains 272 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.0050 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 59 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9771 Z= 0.249 Angle : 0.616 8.527 13248 Z= 0.311 Chirality : 0.042 0.155 1531 Planarity : 0.004 0.086 1660 Dihedral : 5.082 35.181 1392 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.16 % Allowed : 21.89 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.23), residues: 1212 helix: -0.99 (0.26), residues: 384 sheet: -2.31 (0.29), residues: 277 loop : -2.22 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 112 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE R 97 TYR 0.025 0.001 TYR S 178 ARG 0.004 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 32 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7269 (mtm110) REVERT: A 33 GLU cc_start: 0.7722 (mm-30) cc_final: 0.6940 (mm-30) REVERT: A 35 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8272 (mttp) REVERT: A 243 MET cc_start: 0.8819 (mmm) cc_final: 0.8513 (mmm) REVERT: A 304 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 310 LEU cc_start: 0.9189 (mt) cc_final: 0.8710 (mt) REVERT: B 15 LYS cc_start: 0.9071 (tptt) cc_final: 0.8607 (ttmm) REVERT: B 17 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 129 ARG cc_start: 0.7685 (tpp-160) cc_final: 0.7274 (mmm160) REVERT: B 172 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: B 292 PHE cc_start: 0.8138 (m-10) cc_final: 0.7735 (m-80) REVERT: B 325 MET cc_start: 0.8357 (tpp) cc_final: 0.8067 (tpp) REVERT: B 327 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8352 (t) REVERT: C 27 ARG cc_start: 0.7621 (mtt90) cc_final: 0.7338 (mtt90) REVERT: R 63 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7439 (mm) REVERT: R 99 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8601 (mm) REVERT: R 125 LEU cc_start: 0.8322 (tp) cc_final: 0.7880 (tp) REVERT: R 126 LYS cc_start: 0.7474 (tppt) cc_final: 0.7032 (tppt) REVERT: R 137 LEU cc_start: 0.8154 (mp) cc_final: 0.7921 (mp) REVERT: R 209 MET cc_start: 0.7688 (mmm) cc_final: 0.7154 (mmm) REVERT: R 216 GLN cc_start: 0.7638 (tp40) cc_final: 0.6782 (tm-30) REVERT: R 226 ILE cc_start: 0.8875 (tt) cc_final: 0.8471 (tt) REVERT: R 242 HIS cc_start: 0.7620 (p90) cc_final: 0.7409 (p-80) REVERT: S 3 GLN cc_start: 0.7958 (pt0) cc_final: 0.7711 (pt0) REVERT: S 47 TRP cc_start: 0.8343 (t60) cc_final: 0.8137 (t60) REVERT: S 86 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8962 (pp) REVERT: S 91 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8013 (t) REVERT: S 163 TYR cc_start: 0.8908 (m-80) cc_final: 0.8645 (m-80) REVERT: S 219 GLN cc_start: 0.9100 (pp30) cc_final: 0.8498 (pp30) REVERT: S 235 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6074 (mm) outliers start: 53 outliers final: 35 residues processed: 275 average time/residue: 0.2113 time to fit residues: 80.4507 Evaluate side-chains 273 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 306 GLN A 347 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9771 Z= 0.319 Angle : 0.651 8.184 13248 Z= 0.329 Chirality : 0.043 0.156 1531 Planarity : 0.004 0.086 1660 Dihedral : 5.239 36.130 1392 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.64 % Allowed : 23.64 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.23), residues: 1212 helix: -0.64 (0.27), residues: 383 sheet: -2.22 (0.30), residues: 269 loop : -2.12 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 112 HIS 0.005 0.001 HIS A 244 PHE 0.016 0.002 PHE R 97 TYR 0.028 0.002 TYR S 178 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 236 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8570 (m-30) cc_final: 0.8146 (t0) REVERT: A 32 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7365 (mtm110) REVERT: A 33 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6597 (mm-30) REVERT: A 35 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8354 (mttp) REVERT: A 277 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7752 (ttmt) REVERT: A 304 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 310 LEU cc_start: 0.9260 (mt) cc_final: 0.8663 (mt) REVERT: A 331 ASN cc_start: 0.8603 (p0) cc_final: 0.8359 (p0) REVERT: B 9 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7481 (mp10) REVERT: B 15 LYS cc_start: 0.9058 (tptt) cc_final: 0.8600 (ttmm) REVERT: B 17 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 129 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.7200 (mmm160) REVERT: B 172 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: B 209 LYS cc_start: 0.8910 (mttm) cc_final: 0.8451 (mttt) REVERT: B 275 SER cc_start: 0.8696 (m) cc_final: 0.8429 (m) REVERT: B 292 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: B 325 MET cc_start: 0.8375 (tpp) cc_final: 0.8107 (tpp) REVERT: R 63 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7506 (mm) REVERT: R 99 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8656 (mm) REVERT: R 126 LYS cc_start: 0.7360 (tppt) cc_final: 0.6799 (tppt) REVERT: R 209 MET cc_start: 0.7688 (mmm) cc_final: 0.7205 (mmm) REVERT: R 216 GLN cc_start: 0.7785 (tp40) cc_final: 0.7022 (tm-30) REVERT: R 267 TYR cc_start: 0.8516 (t80) cc_final: 0.7911 (t80) REVERT: S 3 GLN cc_start: 0.7946 (pt0) cc_final: 0.7713 (pt0) REVERT: S 20 LEU cc_start: 0.7951 (mm) cc_final: 0.7544 (mm) REVERT: S 47 TRP cc_start: 0.8377 (t60) cc_final: 0.8033 (t60) REVERT: S 86 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8847 (pp) REVERT: S 219 GLN cc_start: 0.9080 (pp30) cc_final: 0.8499 (pp30) REVERT: S 235 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.6075 (mm) outliers start: 58 outliers final: 40 residues processed: 273 average time/residue: 0.2093 time to fit residues: 79.2533 Evaluate side-chains 275 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 229 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9771 Z= 0.200 Angle : 0.606 9.053 13248 Z= 0.301 Chirality : 0.042 0.188 1531 Planarity : 0.004 0.085 1660 Dihedral : 5.017 35.606 1392 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.25 % Allowed : 24.71 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.23), residues: 1212 helix: -0.34 (0.27), residues: 380 sheet: -2.03 (0.30), residues: 275 loop : -2.04 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 112 HIS 0.002 0.001 HIS B 91 PHE 0.013 0.001 PHE R 97 TYR 0.023 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 245 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8552 (m-30) cc_final: 0.8157 (t0) REVERT: A 32 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7688 (mtm110) REVERT: A 35 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8384 (mttp) REVERT: A 186 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 243 MET cc_start: 0.8850 (mmm) cc_final: 0.8591 (mmm) REVERT: A 277 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7633 (ttmt) REVERT: A 304 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 310 LEU cc_start: 0.9247 (mt) cc_final: 0.8619 (mt) REVERT: A 331 ASN cc_start: 0.8608 (p0) cc_final: 0.8375 (p0) REVERT: B 9 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7670 (mp10) REVERT: B 15 LYS cc_start: 0.9064 (tptt) cc_final: 0.8560 (ttmm) REVERT: B 17 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 61 MET cc_start: 0.8329 (ppp) cc_final: 0.7556 (ppp) REVERT: B 129 ARG cc_start: 0.7676 (tpp-160) cc_final: 0.7264 (mmm160) REVERT: B 209 LYS cc_start: 0.8840 (mttm) cc_final: 0.8405 (mttt) REVERT: B 275 SER cc_start: 0.8721 (m) cc_final: 0.8468 (m) REVERT: B 292 PHE cc_start: 0.8123 (m-10) cc_final: 0.7606 (m-80) REVERT: B 325 MET cc_start: 0.8387 (tpp) cc_final: 0.8023 (tpp) REVERT: C 58 GLU cc_start: 0.8253 (pt0) cc_final: 0.7946 (pm20) REVERT: R 63 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7462 (mm) REVERT: R 95 LEU cc_start: 0.8534 (tp) cc_final: 0.8188 (mt) REVERT: R 99 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8278 (mm) REVERT: R 112 TRP cc_start: 0.6191 (t-100) cc_final: 0.5982 (t-100) REVERT: R 126 LYS cc_start: 0.7197 (tppt) cc_final: 0.6803 (tppt) REVERT: R 209 MET cc_start: 0.7720 (mmm) cc_final: 0.7236 (mmm) REVERT: R 216 GLN cc_start: 0.7725 (tp40) cc_final: 0.7234 (tm-30) REVERT: R 226 ILE cc_start: 0.8890 (tt) cc_final: 0.8480 (tt) REVERT: R 242 HIS cc_start: 0.7598 (p90) cc_final: 0.7225 (p-80) REVERT: R 267 TYR cc_start: 0.8482 (t80) cc_final: 0.7734 (t80) REVERT: R 319 GLN cc_start: 0.6512 (tp-100) cc_final: 0.6200 (tp-100) REVERT: S 3 GLN cc_start: 0.7871 (pt0) cc_final: 0.7632 (pt0) REVERT: S 47 TRP cc_start: 0.8283 (t60) cc_final: 0.7964 (t60) REVERT: S 86 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8933 (pp) REVERT: S 91 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8033 (t) REVERT: S 219 GLN cc_start: 0.9056 (pp30) cc_final: 0.8450 (pp30) outliers start: 54 outliers final: 40 residues processed: 279 average time/residue: 0.2199 time to fit residues: 84.5631 Evaluate side-chains 272 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 228 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 0.0170 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9771 Z= 0.411 Angle : 0.703 10.324 13248 Z= 0.353 Chirality : 0.046 0.206 1531 Planarity : 0.004 0.086 1660 Dihedral : 5.505 35.809 1392 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.25 % Allowed : 24.42 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.23), residues: 1212 helix: -0.39 (0.27), residues: 382 sheet: -2.09 (0.31), residues: 265 loop : -2.09 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 111 HIS 0.006 0.001 HIS B 54 PHE 0.019 0.002 PHE R 97 TYR 0.032 0.002 TYR S 178 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8644 (m-30) cc_final: 0.8106 (t0) REVERT: A 32 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7377 (mtm110) REVERT: A 33 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 186 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 243 MET cc_start: 0.8992 (mmm) cc_final: 0.8411 (mmm) REVERT: A 277 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7677 (ttmt) REVERT: A 304 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 310 LEU cc_start: 0.9258 (mt) cc_final: 0.8982 (mt) REVERT: A 331 ASN cc_start: 0.8639 (p0) cc_final: 0.8424 (p0) REVERT: A 347 ASN cc_start: 0.8647 (m-40) cc_final: 0.8399 (m-40) REVERT: B 9 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7641 (mp10) REVERT: B 15 LYS cc_start: 0.9038 (tptt) cc_final: 0.8563 (ttmm) REVERT: B 17 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 61 MET cc_start: 0.8437 (ppp) cc_final: 0.7711 (ppp) REVERT: B 129 ARG cc_start: 0.7577 (tpp-160) cc_final: 0.7183 (mmm160) REVERT: B 215 GLU cc_start: 0.8791 (mp0) cc_final: 0.8567 (mp0) REVERT: B 258 ASP cc_start: 0.7202 (t0) cc_final: 0.6982 (t0) REVERT: B 275 SER cc_start: 0.8911 (m) cc_final: 0.8668 (m) REVERT: B 292 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: B 325 MET cc_start: 0.8411 (tpp) cc_final: 0.8130 (tpp) REVERT: R 63 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7562 (mm) REVERT: R 209 MET cc_start: 0.7733 (mmm) cc_final: 0.7275 (mmm) REVERT: R 216 GLN cc_start: 0.7742 (tp40) cc_final: 0.7284 (tm-30) REVERT: R 250 MET cc_start: 0.8101 (mtm) cc_final: 0.7761 (mtp) REVERT: R 267 TYR cc_start: 0.8615 (t80) cc_final: 0.8128 (t80) REVERT: S 3 GLN cc_start: 0.8063 (pt0) cc_final: 0.7846 (pt0) REVERT: S 47 TRP cc_start: 0.8430 (t60) cc_final: 0.7975 (t60) REVERT: S 171 GLN cc_start: 0.8311 (pt0) cc_final: 0.8067 (pp30) REVERT: S 219 GLN cc_start: 0.9117 (pp30) cc_final: 0.8581 (pp30) outliers start: 54 outliers final: 42 residues processed: 258 average time/residue: 0.2378 time to fit residues: 82.7137 Evaluate side-chains 251 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 163 LYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9771 Z= 0.172 Angle : 0.613 9.406 13248 Z= 0.304 Chirality : 0.042 0.164 1531 Planarity : 0.004 0.084 1660 Dihedral : 5.026 39.093 1392 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.57 % Allowed : 24.90 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.24), residues: 1212 helix: -0.09 (0.27), residues: 380 sheet: -1.99 (0.31), residues: 264 loop : -1.94 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 112 HIS 0.005 0.001 HIS D 18 PHE 0.012 0.001 PHE R 97 TYR 0.023 0.001 TYR S 178 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 249 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8555 (m-30) cc_final: 0.8071 (t0) REVERT: A 32 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7450 (mtm110) REVERT: A 277 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7580 (ttmt) REVERT: A 304 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 310 LEU cc_start: 0.9273 (mt) cc_final: 0.8614 (mt) REVERT: A 331 ASN cc_start: 0.8582 (p0) cc_final: 0.8376 (p0) REVERT: B 15 LYS cc_start: 0.9028 (tptt) cc_final: 0.8559 (ttmm) REVERT: B 17 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 61 MET cc_start: 0.8345 (ppp) cc_final: 0.7635 (ppp) REVERT: B 129 ARG cc_start: 0.7648 (tpp-160) cc_final: 0.7213 (mmm160) REVERT: B 171 ILE cc_start: 0.8425 (mm) cc_final: 0.8170 (mm) REVERT: B 209 LYS cc_start: 0.8917 (mttm) cc_final: 0.8494 (mttt) REVERT: B 275 SER cc_start: 0.8862 (m) cc_final: 0.8633 (m) REVERT: B 292 PHE cc_start: 0.8200 (m-10) cc_final: 0.7673 (m-80) REVERT: B 325 MET cc_start: 0.8343 (tpp) cc_final: 0.8007 (tpp) REVERT: R 63 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7493 (mm) REVERT: R 209 MET cc_start: 0.7674 (mmm) cc_final: 0.7234 (mmm) REVERT: R 216 GLN cc_start: 0.7539 (tp40) cc_final: 0.7265 (tm-30) REVERT: R 226 ILE cc_start: 0.8874 (tt) cc_final: 0.8455 (tt) REVERT: R 250 MET cc_start: 0.8053 (mtm) cc_final: 0.7749 (mtp) REVERT: R 267 TYR cc_start: 0.8516 (t80) cc_final: 0.7965 (t80) REVERT: R 293 ASP cc_start: 0.8981 (t0) cc_final: 0.8751 (t0) REVERT: S 3 GLN cc_start: 0.7931 (pt0) cc_final: 0.7712 (pt0) REVERT: S 47 TRP cc_start: 0.8264 (t60) cc_final: 0.8009 (t60) REVERT: S 219 GLN cc_start: 0.9052 (pp30) cc_final: 0.8409 (pp30) outliers start: 47 outliers final: 35 residues processed: 275 average time/residue: 0.2139 time to fit residues: 80.4447 Evaluate side-chains 266 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.0040 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.0270 overall best weight: 0.5852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9771 Z= 0.166 Angle : 0.621 10.312 13248 Z= 0.305 Chirality : 0.042 0.149 1531 Planarity : 0.004 0.085 1660 Dihedral : 4.903 40.089 1392 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.50 % Allowed : 26.26 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.24), residues: 1212 helix: 0.10 (0.27), residues: 379 sheet: -1.92 (0.30), residues: 278 loop : -1.88 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP S 111 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE S 68 TYR 0.022 0.001 TYR A 296 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 243 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8518 (m-30) cc_final: 0.8045 (t0) REVERT: A 32 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7443 (mtm110) REVERT: A 277 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7447 (ttmt) REVERT: A 304 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 310 LEU cc_start: 0.9251 (mt) cc_final: 0.8582 (mt) REVERT: B 15 LYS cc_start: 0.9071 (tptt) cc_final: 0.8618 (ttmm) REVERT: B 17 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 61 MET cc_start: 0.8322 (ppp) cc_final: 0.7603 (ppp) REVERT: B 129 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7197 (mmm160) REVERT: B 171 ILE cc_start: 0.8295 (mm) cc_final: 0.8054 (mm) REVERT: B 275 SER cc_start: 0.8879 (m) cc_final: 0.8645 (m) REVERT: B 292 PHE cc_start: 0.8078 (m-10) cc_final: 0.7514 (m-80) REVERT: B 325 MET cc_start: 0.8350 (tpp) cc_final: 0.8016 (tpp) REVERT: R 63 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7523 (mm) REVERT: R 209 MET cc_start: 0.7639 (mmm) cc_final: 0.7226 (mmm) REVERT: R 216 GLN cc_start: 0.7532 (tp40) cc_final: 0.7283 (tm-30) REVERT: R 226 ILE cc_start: 0.8862 (tt) cc_final: 0.8438 (tt) REVERT: R 250 MET cc_start: 0.8047 (mtm) cc_final: 0.7757 (mtp) REVERT: R 267 TYR cc_start: 0.8551 (t80) cc_final: 0.8006 (t80) REVERT: R 293 ASP cc_start: 0.9002 (t0) cc_final: 0.8767 (t0) REVERT: S 47 TRP cc_start: 0.8244 (t60) cc_final: 0.8017 (t60) REVERT: S 91 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8022 (t) REVERT: S 219 GLN cc_start: 0.9074 (pp30) cc_final: 0.8384 (pp30) outliers start: 36 outliers final: 28 residues processed: 267 average time/residue: 0.2173 time to fit residues: 80.3636 Evaluate side-chains 258 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 0.0170 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9771 Z= 0.221 Angle : 0.646 10.685 13248 Z= 0.318 Chirality : 0.043 0.145 1531 Planarity : 0.004 0.084 1660 Dihedral : 4.980 42.323 1392 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.89 % Allowed : 26.26 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1212 helix: 0.16 (0.27), residues: 379 sheet: -1.83 (0.30), residues: 275 loop : -1.90 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 112 HIS 0.003 0.001 HIS A 195 PHE 0.035 0.001 PHE S 68 TYR 0.022 0.001 TYR S 178 ARG 0.005 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8537 (m-30) cc_final: 0.8064 (t0) REVERT: A 32 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.7440 (mtm110) REVERT: A 277 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7426 (ttmt) REVERT: A 304 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 310 LEU cc_start: 0.9258 (mt) cc_final: 0.8759 (mt) REVERT: B 15 LYS cc_start: 0.9079 (tptt) cc_final: 0.8832 (mmmt) REVERT: B 17 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 61 MET cc_start: 0.8327 (ppp) cc_final: 0.7585 (ppp) REVERT: B 129 ARG cc_start: 0.7662 (tpp-160) cc_final: 0.7233 (mmm160) REVERT: B 171 ILE cc_start: 0.8441 (mm) cc_final: 0.8146 (mm) REVERT: B 275 SER cc_start: 0.8911 (m) cc_final: 0.8675 (m) REVERT: B 292 PHE cc_start: 0.8200 (m-10) cc_final: 0.7611 (m-80) REVERT: B 325 MET cc_start: 0.8366 (tpp) cc_final: 0.8018 (tpp) REVERT: R 63 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7430 (mm) REVERT: R 126 LYS cc_start: 0.7018 (tppt) cc_final: 0.6490 (tppt) REVERT: R 209 MET cc_start: 0.7650 (mmm) cc_final: 0.7293 (mmm) REVERT: R 216 GLN cc_start: 0.7547 (tp40) cc_final: 0.7299 (tm-30) REVERT: R 226 ILE cc_start: 0.8861 (tt) cc_final: 0.8439 (tt) REVERT: R 250 MET cc_start: 0.8051 (mtm) cc_final: 0.7757 (mtp) REVERT: R 267 TYR cc_start: 0.8573 (t80) cc_final: 0.8038 (t80) REVERT: R 293 ASP cc_start: 0.8970 (t0) cc_final: 0.8733 (t0) REVERT: S 47 TRP cc_start: 0.8305 (t60) cc_final: 0.8040 (t60) REVERT: S 91 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8017 (t) REVERT: S 219 GLN cc_start: 0.9045 (pp30) cc_final: 0.8372 (pp30) outliers start: 40 outliers final: 34 residues processed: 260 average time/residue: 0.2145 time to fit residues: 76.8827 Evaluate side-chains 256 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 0.0570 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124833 restraints weight = 14544.071| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.92 r_work: 0.3502 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9771 Z= 0.179 Angle : 0.625 10.188 13248 Z= 0.307 Chirality : 0.042 0.143 1531 Planarity : 0.004 0.084 1660 Dihedral : 4.893 44.458 1392 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.28 % Allowed : 26.07 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.24), residues: 1212 helix: 0.25 (0.27), residues: 381 sheet: -1.76 (0.30), residues: 277 loop : -1.85 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 112 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE R 97 TYR 0.021 0.001 TYR A 296 ARG 0.005 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.81 seconds wall clock time: 45 minutes 6.31 seconds (2706.31 seconds total)