Starting phenix.real_space_refine on Thu May 15 23:44:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1z_39741/05_2025/8z1z_39741_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1z_39741/05_2025/8z1z_39741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1z_39741/05_2025/8z1z_39741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1z_39741/05_2025/8z1z_39741.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1z_39741/05_2025/8z1z_39741_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1z_39741/05_2025/8z1z_39741_neut.cif" } resolution = 3.26 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 6 5.49 5 S 94 5.16 5 C 8731 2.51 5 N 2342 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13652 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2317 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "B" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2187 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 17, 'TRANS': 271} Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2486 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 20, 'TRANS': 303} Chain: "D" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2537 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 22, 'TRANS': 299} Chain: "F" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4047 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 31, 'TRANS': 475} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6670 SG CYS C 284 57.640 65.787 136.788 1.00107.90 S ATOM 6718 SG CYS C 290 53.194 65.389 141.834 1.00100.35 S ATOM 6774 SG CYS C 297 57.956 69.705 141.609 1.00127.91 S ATOM 6910 SG CYS C 315 59.396 63.455 142.612 1.00114.80 S ATOM 9341 SG CYS D 306 29.848 13.415 135.683 1.00126.80 S ATOM 9470 SG CYS D 323 27.865 19.694 138.497 1.00115.11 S ATOM 9234 SG CYS D 293 29.203 18.694 132.171 1.00108.26 S ATOM 9280 SG CYS D 299 33.837 18.064 137.451 1.00119.19 S Time building chain proxies: 7.97, per 1000 atoms: 0.58 Number of scatterers: 13652 At special positions: 0 Unit cell: (86.32, 93.6, 162.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 94 16.00 P 6 15.00 O 2471 8.00 N 2342 7.00 C 8731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 262 " distance=1.98 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 401 " pdb="FE4 SF4 C 401 " - pdb=" SG CYS C 315 " pdb="FE3 SF4 C 401 " - pdb=" SG CYS C 297 " pdb="FE2 SF4 C 401 " - pdb=" SG CYS C 290 " pdb="FE1 SF4 C 401 " - pdb=" SG CYS C 284 " pdb=" SF4 D 401 " pdb="FE2 SF4 D 401 " - pdb=" SG CYS D 323 " pdb="FE4 SF4 D 401 " - pdb=" SG CYS D 299 " pdb="FE3 SF4 D 401 " - pdb=" SG CYS D 293 " pdb="FE1 SF4 D 401 " - pdb=" SG CYS D 306 " Number of angles added : 24 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 10 sheets defined 55.5% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 11 through 28 Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.531A pdb=" N TRP A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 113 Proline residue: A 94 - end of helix removed outlier: 3.852A pdb=" N ALA A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 removed outlier: 4.038A pdb=" N ALA A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 143 removed outlier: 3.537A pdb=" N MET A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.571A pdb=" N TRP A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 205 through 233 removed outlier: 4.628A pdb=" N ILE A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.854A pdb=" N VAL A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 254 through 277 removed outlier: 4.228A pdb=" N ASN A 258 " --> pdb=" O HIS A 254 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.986A pdb=" N TRP A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.567A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'B' and resid 17 through 28 removed outlier: 3.987A pdb=" N ARG B 28 " --> pdb=" O HIS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 53 removed outlier: 3.538A pdb=" N VAL B 33 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.175A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 126 removed outlier: 4.543A pdb=" N ARG B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 144 Processing helix chain 'B' and resid 145 through 157 removed outlier: 3.754A pdb=" N ALA B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 188 removed outlier: 4.164A pdb=" N ALA B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 4.302A pdb=" N VAL B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.728A pdb=" N THR B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 215 through 240 removed outlier: 4.335A pdb=" N LEU B 219 " --> pdb=" O CYS B 215 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 265 through 293 removed outlier: 4.114A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.771A pdb=" N LEU B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.515A pdb=" N ILE C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.861A pdb=" N ASN C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 107 through 121 removed outlier: 4.184A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.616A pdb=" N ARG C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 203 removed outlier: 4.204A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 221 removed outlier: 4.385A pdb=" N VAL C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 removed outlier: 3.878A pdb=" N PHE C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS C 243 " --> pdb=" O HIS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 256 through 261 removed outlier: 6.182A pdb=" N GLU C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 90 through 100 removed outlier: 4.086A pdb=" N LYS D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.731A pdb=" N GLY D 110 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 133 through 148 removed outlier: 3.501A pdb=" N ARG D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.810A pdb=" N PHE D 162 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.638A pdb=" N ARG D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 211 removed outlier: 4.122A pdb=" N GLN D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.706A pdb=" N VAL D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.526A pdb=" N ALA D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 293 through 298 removed outlier: 4.339A pdb=" N ALA D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.570A pdb=" N LEU F 46 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 57 Processing helix chain 'F' and resid 114 through 127 removed outlier: 3.829A pdb=" N VAL F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 147 removed outlier: 3.551A pdb=" N MET F 146 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 173 through 178 Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 249 through 259 removed outlier: 4.127A pdb=" N LYS F 259 " --> pdb=" O ALA F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 306 through 316 removed outlier: 3.633A pdb=" N ARG F 310 " --> pdb=" O ASP F 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F 314 " --> pdb=" O ARG F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.140A pdb=" N LYS F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 367 Processing helix chain 'F' and resid 388 through 402 Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 439 through 442 Processing helix chain 'F' and resid 443 through 449 Processing helix chain 'F' and resid 464 through 476 removed outlier: 3.699A pdb=" N GLU F 468 " --> pdb=" O TYR F 464 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU F 470 " --> pdb=" O PRO F 466 " (cutoff:3.500A) Proline residue: F 473 - end of helix Processing helix chain 'F' and resid 479 through 498 removed outlier: 3.995A pdb=" N GLU F 485 " --> pdb=" O ASN F 481 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 532 removed outlier: 4.452A pdb=" N ASN F 531 " --> pdb=" O HIS F 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.367A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN C 5 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.367A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN C 5 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.621A pdb=" N ALA C 92 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASP C 178 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE C 94 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 35 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE C 225 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 37 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET C 227 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 39 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 234 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR C 228 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 45 removed outlier: 6.203A pdb=" N LYS D 20 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP D 39 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 18 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL D 41 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE D 16 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE D 43 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN D 14 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 101 through 104 removed outlier: 6.834A pdb=" N GLN D 102 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP D 186 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL D 104 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 232 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS D 243 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 234 " --> pdb=" O VAL D 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 30 through 33 removed outlier: 6.547A pdb=" N LEU F 31 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N SER F 245 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR F 33 " --> pdb=" O SER F 245 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG F 223 " --> pdb=" O TYR F 218 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR F 218 " --> pdb=" O ARG F 223 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG F 225 " --> pdb=" O GLN F 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AA8, first strand: chain 'F' and resid 79 through 84 removed outlier: 3.971A pdb=" N LYS F 81 " --> pdb=" O HIS F 94 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 331 through 333 removed outlier: 4.542A pdb=" N ALA F 500 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU F 295 " --> pdb=" O ALA F 500 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE F 502 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY F 293 " --> pdb=" O ILE F 502 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA F 504 " --> pdb=" O ASN F 291 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ASN F 291 " --> pdb=" O ALA F 504 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER F 506 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET F 285 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASP F 375 " --> pdb=" O THR F 428 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET F 430 " --> pdb=" O ASP F 375 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP F 377 " --> pdb=" O MET F 430 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLY F 432 " --> pdb=" O TRP F 377 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE F 374 " --> pdb=" O LYS F 408 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL F 410 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU F 376 " --> pdb=" O VAL F 410 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 516 through 517 656 hydrogen bonds defined for protein. 1860 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: 3.68 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 6390 1.43 - 1.65: 7402 1.65 - 1.86: 149 1.86 - 2.08: 2 2.08 - 2.30: 24 Bond restraints: 13967 Sorted by residual: bond pdb=" ND1 HIS D 21 " pdb=" CE1 HIS D 21 " ideal model delta sigma weight residual 1.321 1.225 0.096 1.00e-02 1.00e+04 9.22e+01 bond pdb=" CE1 HIS F 94 " pdb=" NE2 HIS F 94 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.86e+01 bond pdb=" CE1 HIS C 239 " pdb=" NE2 HIS C 239 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.85e+01 bond pdb=" ND1 HIS A 75 " pdb=" CE1 HIS A 75 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.83e+01 bond pdb=" CE1 HIS F 102 " pdb=" NE2 HIS F 102 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.70e+01 ... (remaining 13962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 15904 2.98 - 5.95: 2509 5.95 - 8.93: 502 8.93 - 11.91: 68 11.91 - 14.88: 8 Bond angle restraints: 18991 Sorted by residual: angle pdb=" C ASN C 5 " pdb=" N VAL C 6 " pdb=" CA VAL C 6 " ideal model delta sigma weight residual 122.96 130.66 -7.70 9.50e-01 1.11e+00 6.57e+01 angle pdb=" CA HIS F 102 " pdb=" CB HIS F 102 " pdb=" CG HIS F 102 " ideal model delta sigma weight residual 113.80 121.45 -7.65 1.00e+00 1.00e+00 5.86e+01 angle pdb=" CA HIS D 21 " pdb=" CB HIS D 21 " pdb=" CG HIS D 21 " ideal model delta sigma weight residual 113.80 121.45 -7.65 1.00e+00 1.00e+00 5.85e+01 angle pdb=" CA ASP F 103 " pdb=" CB ASP F 103 " pdb=" CG ASP F 103 " ideal model delta sigma weight residual 112.60 120.14 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CA ASP C 237 " pdb=" CB ASP C 237 " pdb=" CG ASP C 237 " ideal model delta sigma weight residual 112.60 120.05 -7.45 1.00e+00 1.00e+00 5.55e+01 ... (remaining 18986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.99: 7842 19.99 - 39.98: 462 39.98 - 59.97: 76 59.97 - 79.96: 22 79.96 - 99.95: 12 Dihedral angle restraints: 8414 sinusoidal: 3403 harmonic: 5011 Sorted by residual: dihedral pdb=" CA PRO F 59 " pdb=" C PRO F 59 " pdb=" N LEU F 60 " pdb=" CA LEU F 60 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA GLN F 214 " pdb=" C GLN F 214 " pdb=" N LEU F 215 " pdb=" CA LEU F 215 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU F 261 " pdb=" C GLU F 261 " pdb=" N CYS F 262 " pdb=" CA CYS F 262 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 8411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1496 0.150 - 0.300: 206 0.300 - 0.450: 119 0.450 - 0.600: 225 0.600 - 0.750: 98 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CG LEU C 9 " pdb=" CB LEU C 9 " pdb=" CD1 LEU C 9 " pdb=" CD2 LEU C 9 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CG LEU B 149 " pdb=" CB LEU B 149 " pdb=" CD1 LEU B 149 " pdb=" CD2 LEU B 149 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CG LEU C 174 " pdb=" CB LEU C 174 " pdb=" CD1 LEU C 174 " pdb=" CD2 LEU C 174 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.35e+01 ... (remaining 2141 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 148 " -0.157 2.00e-02 2.50e+03 8.50e-02 1.81e+02 pdb=" CG TRP A 148 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 148 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 148 " 0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP A 148 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TRP A 148 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 148 " 0.128 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 148 " -0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 148 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 148 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.157 2.00e-02 2.50e+03 8.62e-02 1.48e+02 pdb=" CG TYR A 141 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.051 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " -0.121 2.00e-02 2.50e+03 6.89e-02 1.19e+02 pdb=" CG TRP A 293 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " 0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " -0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " 0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " -0.072 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1207 2.77 - 3.30: 14102 3.30 - 3.84: 21624 3.84 - 4.37: 27335 4.37 - 4.90: 45905 Nonbonded interactions: 110173 Sorted by model distance: nonbonded pdb=" OD1 ASP F 272 " pdb=" NH2 ARG F 275 " model vdw 2.238 3.120 nonbonded pdb=" OH TYR D 316 " pdb=" OD1 ASP D 327 " model vdw 2.321 3.040 nonbonded pdb=" OE1 GLN D 9 " pdb=" O GLN D 10 " model vdw 2.325 3.040 nonbonded pdb=" OE2 GLU D 123 " pdb=" OH TYR D 155 " model vdw 2.327 3.040 nonbonded pdb=" OD1 ASP C 295 " pdb=" NH1 ARG C 298 " model vdw 2.357 3.120 ... (remaining 110168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 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 : 0.028 0.470 13976 Z= 1.461 Angle : 2.399 25.990 19017 Z= 1.553 Chirality : 0.258 0.750 2144 Planarity : 0.015 0.182 2430 Dihedral : 13.943 99.947 5193 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.17 % Allowed : 3.50 % Favored : 95.33 % Cbeta Deviations : 9.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.24 (0.18), residues: 1728 helix: -1.91 (0.15), residues: 818 sheet: -0.51 (0.41), residues: 166 loop : -0.99 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.157 0.019 TRP A 148 HIS 0.013 0.003 HIS D 255 PHE 0.108 0.012 PHE F 182 TYR 0.157 0.023 TYR A 141 ARG 0.011 0.001 ARG F 253 Details of bonding type rmsd hydrogen bonds : bond 0.19683 ( 653) hydrogen bonds : angle 8.05648 ( 1860) metal coordination : bond 0.21566 ( 8) metal coordination : angle 9.32460 ( 24) SS BOND : bond 0.05232 ( 1) SS BOND : angle 0.36727 ( 2) covalent geometry : bond 0.02703 (13967) covalent geometry : angle 2.37814 (18991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 401 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.7929 (mtp) cc_final: 0.7695 (mtp) REVERT: A 152 LEU cc_start: 0.7003 (mt) cc_final: 0.6769 (mt) REVERT: A 155 LEU cc_start: 0.7349 (mp) cc_final: 0.7124 (mp) REVERT: A 172 MET cc_start: 0.7463 (mtm) cc_final: 0.7129 (mtm) REVERT: A 184 PHE cc_start: 0.6853 (m-80) cc_final: 0.6620 (m-10) REVERT: A 257 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7185 (ttt180) REVERT: A 260 MET cc_start: 0.5798 (mmt) cc_final: 0.5087 (mmm) REVERT: B 94 LEU cc_start: 0.4716 (mt) cc_final: 0.4485 (mt) REVERT: B 115 MET cc_start: 0.6190 (mmm) cc_final: 0.5956 (mmm) REVERT: C 32 GLN cc_start: 0.7304 (pm20) cc_final: 0.6932 (pm20) REVERT: C 41 GLU cc_start: 0.6788 (tt0) cc_final: 0.6417 (tt0) REVERT: C 44 SER cc_start: 0.8047 (m) cc_final: 0.7763 (p) REVERT: C 66 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 69 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7438 (mt-10) REVERT: C 73 GLN cc_start: 0.6054 (mp10) cc_final: 0.5267 (mp10) REVERT: C 78 ILE cc_start: 0.6626 (mm) cc_final: 0.6167 (mm) REVERT: C 80 GLU cc_start: 0.6088 (tp30) cc_final: 0.5850 (tp30) REVERT: C 82 GLU cc_start: 0.6864 (tt0) cc_final: 0.6566 (pt0) REVERT: C 83 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.5428 (ptm160) REVERT: C 84 ARG cc_start: 0.6596 (mmm-85) cc_final: 0.6386 (mmm-85) REVERT: C 93 MET cc_start: 0.8061 (ttt) cc_final: 0.7826 (ttt) REVERT: C 111 GLN cc_start: 0.6999 (tp40) cc_final: 0.6697 (tp40) REVERT: C 127 ARG cc_start: 0.7294 (mtp180) cc_final: 0.6920 (ttm110) REVERT: C 129 GLN cc_start: 0.7126 (tm-30) cc_final: 0.6712 (tm-30) REVERT: C 135 LEU cc_start: 0.7155 (mt) cc_final: 0.6893 (mp) REVERT: C 148 ASP cc_start: 0.7829 (m-30) cc_final: 0.7476 (m-30) REVERT: C 168 ILE cc_start: 0.7465 (mt) cc_final: 0.7142 (mp) REVERT: C 175 LEU cc_start: 0.8128 (tt) cc_final: 0.7789 (tt) REVERT: C 186 VAL cc_start: 0.5878 (m) cc_final: 0.5626 (t) REVERT: C 219 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7010 (mt-10) REVERT: C 234 GLU cc_start: 0.7724 (tt0) cc_final: 0.7498 (tt0) REVERT: C 311 ARG cc_start: 0.7155 (mtm180) cc_final: 0.6801 (ttm170) REVERT: C 313 SER cc_start: 0.7827 (p) cc_final: 0.7617 (t) REVERT: D 26 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7664 (mtmm) REVERT: D 28 MET cc_start: 0.5554 (pmm) cc_final: 0.5234 (pmm) REVERT: D 36 LYS cc_start: 0.7616 (mmtp) cc_final: 0.7388 (mmtp) REVERT: D 46 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6893 (mt-10) REVERT: D 145 MET cc_start: 0.7411 (mtm) cc_final: 0.7030 (mtp) REVERT: D 310 GLN cc_start: 0.7643 (pp30) cc_final: 0.7225 (pp30) REVERT: D 314 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7158 (ttmm) REVERT: D 328 GLN cc_start: 0.7410 (tp40) cc_final: 0.7156 (tt0) REVERT: F 35 SER cc_start: 0.8354 (t) cc_final: 0.7878 (p) REVERT: F 36 GLU cc_start: 0.7205 (tp30) cc_final: 0.6447 (tp30) REVERT: F 108 LYS cc_start: 0.7405 (tptp) cc_final: 0.7188 (tptp) REVERT: F 150 GLU cc_start: 0.6180 (tp30) cc_final: 0.5826 (tp30) REVERT: F 156 LYS cc_start: 0.7465 (mtmt) cc_final: 0.6835 (ptmm) REVERT: F 238 GLN cc_start: 0.7959 (mp10) cc_final: 0.7683 (mp10) REVERT: F 252 VAL cc_start: 0.7791 (t) cc_final: 0.7390 (p) REVERT: F 276 MET cc_start: 0.6809 (mtp) cc_final: 0.6589 (mtm) REVERT: F 278 GLN cc_start: 0.7255 (tp40) cc_final: 0.6996 (mp10) REVERT: F 285 MET cc_start: 0.6866 (mmt) cc_final: 0.5623 (mmt) REVERT: F 347 ASP cc_start: 0.7532 (p0) cc_final: 0.7209 (m-30) REVERT: F 352 TYR cc_start: 0.6217 (m-10) cc_final: 0.5701 (m-10) REVERT: F 388 ASN cc_start: 0.6212 (t0) cc_final: 0.5712 (t0) REVERT: F 395 MET cc_start: 0.6613 (mtp) cc_final: 0.6134 (mtt) REVERT: F 461 LYS cc_start: 0.7863 (tptt) cc_final: 0.7358 (mptt) REVERT: F 470 LEU cc_start: 0.7231 (mt) cc_final: 0.6952 (mt) REVERT: F 510 GLU cc_start: 0.7382 (tt0) cc_final: 0.7162 (tt0) outliers start: 17 outliers final: 10 residues processed: 415 average time/residue: 0.2940 time to fit residues: 167.9696 Evaluate side-chains 359 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 348 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 447 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 258 ASN B 72 GLN B 260 GLN C 179 GLN D 82 GLN D 89 HIS D 154 HIS D 187 GLN F 62 ASN F 125 GLN F 130 ASN ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 269 ASN F 298 ASN F 397 GLN F 495 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.144680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130406 restraints weight = 17955.827| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.92 r_work: 0.3608 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13976 Z= 0.207 Angle : 0.779 26.539 19017 Z= 0.367 Chirality : 0.048 0.213 2144 Planarity : 0.005 0.049 2430 Dihedral : 8.291 99.763 1946 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.78 % Allowed : 9.20 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.01 (0.19), residues: 1728 helix: -0.46 (0.17), residues: 832 sheet: -0.44 (0.39), residues: 178 loop : -0.79 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 293 HIS 0.014 0.001 HIS A 75 PHE 0.019 0.002 PHE D 162 TYR 0.018 0.002 TYR B 55 ARG 0.007 0.001 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 653) hydrogen bonds : angle 5.62514 ( 1860) metal coordination : bond 0.01460 ( 8) metal coordination : angle 9.45914 ( 24) SS BOND : bond 0.00795 ( 1) SS BOND : angle 1.36033 ( 2) covalent geometry : bond 0.00486 (13967) covalent geometry : angle 0.70314 (18991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 340 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LEU cc_start: 0.7685 (mt) cc_final: 0.7313 (mp) REVERT: A 185 MET cc_start: 0.8034 (mmm) cc_final: 0.7644 (tpp) REVERT: A 248 MET cc_start: 0.6844 (ppp) cc_final: 0.6571 (ppp) REVERT: A 260 MET cc_start: 0.6908 (mmt) cc_final: 0.6616 (mmm) REVERT: B 22 PHE cc_start: 0.7792 (t80) cc_final: 0.7580 (t80) REVERT: B 77 MET cc_start: 0.6989 (mmt) cc_final: 0.6427 (mmt) REVERT: B 168 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6780 (mt) REVERT: B 210 ASN cc_start: 0.8661 (m110) cc_final: 0.8349 (m-40) REVERT: C 32 GLN cc_start: 0.7386 (pm20) cc_final: 0.7050 (pm20) REVERT: C 41 GLU cc_start: 0.7011 (tt0) cc_final: 0.6596 (tt0) REVERT: C 64 MET cc_start: 0.7433 (mpp) cc_final: 0.7100 (mpp) REVERT: C 129 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7348 (tm-30) REVERT: C 168 ILE cc_start: 0.8123 (mt) cc_final: 0.7868 (mp) REVERT: C 198 GLU cc_start: 0.6680 (tt0) cc_final: 0.6433 (tt0) REVERT: D 28 MET cc_start: 0.5943 (pmm) cc_final: 0.5521 (pmm) REVERT: D 66 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7514 (mtm-85) REVERT: D 157 ARG cc_start: 0.8327 (mtt180) cc_final: 0.8052 (mmm-85) REVERT: D 314 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7999 (ttmm) REVERT: F 35 SER cc_start: 0.8830 (t) cc_final: 0.8626 (p) REVERT: F 42 PHE cc_start: 0.7878 (m-80) cc_final: 0.7677 (m-80) REVERT: F 67 PHE cc_start: 0.7496 (m-80) cc_final: 0.7241 (m-80) REVERT: F 87 ASP cc_start: 0.8100 (t0) cc_final: 0.7890 (t0) REVERT: F 108 LYS cc_start: 0.7474 (tptp) cc_final: 0.7272 (tptp) REVERT: F 135 VAL cc_start: 0.7314 (t) cc_final: 0.7025 (p) REVERT: F 391 ARG cc_start: 0.7027 (mmp80) cc_final: 0.6707 (mmp80) REVERT: F 470 LEU cc_start: 0.8007 (mt) cc_final: 0.7753 (mt) REVERT: F 528 HIS cc_start: 0.8420 (m-70) cc_final: 0.8127 (m90) outliers start: 26 outliers final: 19 residues processed: 356 average time/residue: 0.2992 time to fit residues: 146.9803 Evaluate side-chains 343 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 323 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 515 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 124 optimal weight: 0.0980 chunk 59 optimal weight: 0.3980 chunk 166 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 258 ASN A 270 GLN C 111 GLN C 179 GLN C 212 HIS F 114 ASN F 130 ASN ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 GLN F 527 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130512 restraints weight = 17915.982| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.94 r_work: 0.3612 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13976 Z= 0.165 Angle : 0.700 23.148 19017 Z= 0.326 Chirality : 0.045 0.283 2144 Planarity : 0.005 0.047 2430 Dihedral : 7.718 91.376 1931 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.95 % Allowed : 12.83 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.73 (0.20), residues: 1728 helix: -0.10 (0.17), residues: 846 sheet: -0.47 (0.40), residues: 178 loop : -0.80 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.005 0.001 HIS F 133 PHE 0.020 0.002 PHE A 184 TYR 0.016 0.002 TYR F 354 ARG 0.013 0.001 ARG D 298 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 653) hydrogen bonds : angle 5.19322 ( 1860) metal coordination : bond 0.01017 ( 8) metal coordination : angle 8.41709 ( 24) SS BOND : bond 0.00528 ( 1) SS BOND : angle 1.40042 ( 2) covalent geometry : bond 0.00386 (13967) covalent geometry : angle 0.63290 (18991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 335 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.6665 (ptp) cc_final: 0.6427 (ptp) REVERT: A 152 LEU cc_start: 0.7634 (mt) cc_final: 0.7333 (mt) REVERT: A 189 THR cc_start: 0.8413 (p) cc_final: 0.8197 (p) REVERT: A 248 MET cc_start: 0.6764 (ppp) cc_final: 0.6457 (ppp) REVERT: A 303 TYR cc_start: 0.8393 (m-80) cc_final: 0.8183 (m-80) REVERT: B 22 PHE cc_start: 0.7810 (t80) cc_final: 0.7603 (t80) REVERT: B 77 MET cc_start: 0.7093 (mmt) cc_final: 0.6530 (mmt) REVERT: B 168 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6822 (mm) REVERT: B 210 ASN cc_start: 0.8676 (m110) cc_final: 0.8307 (m-40) REVERT: B 239 PHE cc_start: 0.6929 (t80) cc_final: 0.6427 (t80) REVERT: C 32 GLN cc_start: 0.7366 (pm20) cc_final: 0.7045 (pm20) REVERT: C 41 GLU cc_start: 0.6860 (tt0) cc_final: 0.6550 (tt0) REVERT: C 54 MET cc_start: 0.5842 (mmt) cc_final: 0.5585 (mmm) REVERT: C 64 MET cc_start: 0.7432 (mpp) cc_final: 0.7103 (mpp) REVERT: C 80 GLU cc_start: 0.7056 (tp30) cc_final: 0.6818 (tp30) REVERT: C 129 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 168 ILE cc_start: 0.8114 (mt) cc_final: 0.7869 (mp) REVERT: C 198 GLU cc_start: 0.6666 (tt0) cc_final: 0.6431 (tt0) REVERT: D 314 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7833 (mmmm) REVERT: F 35 SER cc_start: 0.8791 (t) cc_final: 0.8560 (p) REVERT: F 36 GLU cc_start: 0.7769 (tp30) cc_final: 0.7309 (tp30) REVERT: F 87 ASP cc_start: 0.8112 (t0) cc_final: 0.7811 (t0) REVERT: F 108 LYS cc_start: 0.7493 (tptp) cc_final: 0.7267 (tptp) REVERT: F 135 VAL cc_start: 0.7309 (t) cc_final: 0.7062 (p) REVERT: F 146 MET cc_start: 0.6317 (tpt) cc_final: 0.6056 (tpt) REVERT: F 254 TYR cc_start: 0.8409 (t80) cc_final: 0.8037 (t80) REVERT: F 265 MET cc_start: 0.7969 (ttt) cc_final: 0.7731 (ptm) REVERT: F 391 ARG cc_start: 0.6846 (mmp80) cc_final: 0.6500 (mmp80) REVERT: F 470 LEU cc_start: 0.7844 (mt) cc_final: 0.7571 (mt) REVERT: F 530 GLU cc_start: 0.7283 (pm20) cc_final: 0.6239 (pm20) outliers start: 43 outliers final: 25 residues processed: 354 average time/residue: 0.2952 time to fit residues: 144.9984 Evaluate side-chains 345 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 319 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 515 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 133 optimal weight: 0.8980 chunk 120 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN C 312 GLN D 160 HIS ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.129681 restraints weight = 17828.313| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.93 r_work: 0.3599 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13976 Z= 0.190 Angle : 0.697 22.672 19017 Z= 0.319 Chirality : 0.045 0.182 2144 Planarity : 0.005 0.048 2430 Dihedral : 7.581 86.724 1929 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.09 % Allowed : 14.21 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.66 (0.20), residues: 1728 helix: 0.03 (0.18), residues: 836 sheet: -0.49 (0.40), residues: 178 loop : -0.85 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 293 HIS 0.006 0.001 HIS F 133 PHE 0.016 0.002 PHE B 44 TYR 0.013 0.002 TYR F 345 ARG 0.005 0.001 ARG F 310 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 653) hydrogen bonds : angle 5.10958 ( 1860) metal coordination : bond 0.01249 ( 8) metal coordination : angle 8.70154 ( 24) SS BOND : bond 0.00708 ( 1) SS BOND : angle 1.25782 ( 2) covalent geometry : bond 0.00449 (13967) covalent geometry : angle 0.62552 (18991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 335 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6686 (mmm) cc_final: 0.6469 (mmm) REVERT: A 248 MET cc_start: 0.6782 (ppp) cc_final: 0.6482 (ppp) REVERT: A 303 TYR cc_start: 0.8429 (m-80) cc_final: 0.8117 (m-80) REVERT: B 77 MET cc_start: 0.7160 (mmt) cc_final: 0.6608 (mmt) REVERT: B 168 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6797 (mm) REVERT: B 210 ASN cc_start: 0.8718 (m110) cc_final: 0.8378 (m-40) REVERT: B 239 PHE cc_start: 0.7032 (t80) cc_final: 0.6478 (t80) REVERT: B 254 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: C 32 GLN cc_start: 0.7372 (pm20) cc_final: 0.7085 (pm20) REVERT: C 41 GLU cc_start: 0.6923 (tt0) cc_final: 0.6663 (tt0) REVERT: C 54 MET cc_start: 0.5913 (mmt) cc_final: 0.5676 (mmp) REVERT: C 64 MET cc_start: 0.7416 (mpp) cc_final: 0.7030 (mpp) REVERT: C 69 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 80 GLU cc_start: 0.7085 (tp30) cc_final: 0.6831 (tp30) REVERT: C 129 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7403 (tm-30) REVERT: C 168 ILE cc_start: 0.8158 (mt) cc_final: 0.7911 (mp) REVERT: C 198 GLU cc_start: 0.6701 (tt0) cc_final: 0.6459 (tt0) REVERT: C 298 ARG cc_start: 0.7149 (mtm180) cc_final: 0.6892 (mtt90) REVERT: D 145 MET cc_start: 0.7356 (mtm) cc_final: 0.7073 (mtp) REVERT: D 314 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7832 (mmmm) REVERT: F 35 SER cc_start: 0.8808 (t) cc_final: 0.8570 (p) REVERT: F 74 VAL cc_start: 0.7695 (t) cc_final: 0.7356 (m) REVERT: F 83 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6736 (mt-10) REVERT: F 87 ASP cc_start: 0.8180 (t0) cc_final: 0.7881 (t0) REVERT: F 108 LYS cc_start: 0.7505 (tptp) cc_final: 0.7270 (tptp) REVERT: F 112 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6961 (mp0) REVERT: F 135 VAL cc_start: 0.7315 (t) cc_final: 0.7090 (p) REVERT: F 156 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7740 (ptmm) REVERT: F 254 TYR cc_start: 0.8424 (t80) cc_final: 0.8081 (t80) REVERT: F 265 MET cc_start: 0.8025 (ttt) cc_final: 0.7818 (ptm) REVERT: F 470 LEU cc_start: 0.7860 (mt) cc_final: 0.7586 (mt) REVERT: F 530 GLU cc_start: 0.7939 (pm20) cc_final: 0.6716 (pm20) outliers start: 45 outliers final: 29 residues processed: 357 average time/residue: 0.2965 time to fit residues: 147.7008 Evaluate side-chains 358 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 327 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 534 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 158 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 157 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN C 111 GLN C 287 ASN C 312 GLN F 161 ASN ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129739 restraints weight = 17898.392| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.94 r_work: 0.3601 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13976 Z= 0.179 Angle : 0.692 20.691 19017 Z= 0.314 Chirality : 0.044 0.184 2144 Planarity : 0.005 0.047 2430 Dihedral : 7.502 86.312 1929 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.36 % Allowed : 15.10 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.20), residues: 1728 helix: 0.10 (0.18), residues: 845 sheet: -0.44 (0.41), residues: 176 loop : -0.85 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 293 HIS 0.007 0.001 HIS F 133 PHE 0.014 0.001 PHE D 162 TYR 0.012 0.002 TYR C 249 ARG 0.011 0.000 ARG F 310 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 653) hydrogen bonds : angle 5.02804 ( 1860) metal coordination : bond 0.01264 ( 8) metal coordination : angle 8.50780 ( 24) SS BOND : bond 0.00658 ( 1) SS BOND : angle 1.12337 ( 2) covalent geometry : bond 0.00424 (13967) covalent geometry : angle 0.62311 (18991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 339 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6677 (mmm) cc_final: 0.6467 (mmm) REVERT: A 248 MET cc_start: 0.6748 (ppp) cc_final: 0.6527 (ppp) REVERT: A 303 TYR cc_start: 0.8421 (m-80) cc_final: 0.8019 (m-80) REVERT: B 77 MET cc_start: 0.7206 (mmt) cc_final: 0.6645 (mmt) REVERT: B 168 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6715 (mm) REVERT: B 210 ASN cc_start: 0.8709 (m110) cc_final: 0.8384 (m-40) REVERT: B 239 PHE cc_start: 0.7090 (t80) cc_final: 0.6531 (t80) REVERT: B 254 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7872 (ttm) REVERT: C 26 ILE cc_start: 0.8606 (pt) cc_final: 0.8392 (pt) REVERT: C 32 GLN cc_start: 0.7343 (pm20) cc_final: 0.7056 (pm20) REVERT: C 41 GLU cc_start: 0.6929 (tt0) cc_final: 0.6656 (tt0) REVERT: C 62 ARG cc_start: 0.8112 (ptt-90) cc_final: 0.7582 (ptt-90) REVERT: C 64 MET cc_start: 0.7431 (mpp) cc_final: 0.7032 (mpp) REVERT: C 69 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7706 (mt-10) REVERT: C 80 GLU cc_start: 0.7068 (tp30) cc_final: 0.6849 (tp30) REVERT: C 129 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7332 (tm-30) REVERT: C 168 ILE cc_start: 0.8171 (mt) cc_final: 0.7921 (mp) REVERT: C 198 GLU cc_start: 0.6712 (tt0) cc_final: 0.6458 (tt0) REVERT: C 205 MET cc_start: 0.8169 (ttt) cc_final: 0.7859 (ttt) REVERT: D 145 MET cc_start: 0.7400 (mtm) cc_final: 0.7114 (mtp) REVERT: D 314 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7832 (mmmm) REVERT: F 35 SER cc_start: 0.8818 (t) cc_final: 0.8548 (p) REVERT: F 36 GLU cc_start: 0.7772 (tp30) cc_final: 0.7473 (tp30) REVERT: F 74 VAL cc_start: 0.7658 (t) cc_final: 0.7316 (m) REVERT: F 83 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6880 (mt-10) REVERT: F 87 ASP cc_start: 0.8217 (t0) cc_final: 0.7893 (t0) REVERT: F 108 LYS cc_start: 0.7500 (tptp) cc_final: 0.7263 (tptp) REVERT: F 112 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7092 (mm-30) REVERT: F 135 VAL cc_start: 0.7276 (t) cc_final: 0.7069 (p) REVERT: F 146 MET cc_start: 0.6381 (tpt) cc_final: 0.6163 (tpp) REVERT: F 156 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7855 (ptmt) REVERT: F 254 TYR cc_start: 0.8450 (t80) cc_final: 0.8001 (t80) REVERT: F 276 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.6043 (mpp) REVERT: F 297 TYR cc_start: 0.7099 (m-80) cc_final: 0.6806 (m-10) REVERT: F 354 TYR cc_start: 0.6904 (t80) cc_final: 0.6537 (t80) REVERT: F 470 LEU cc_start: 0.7876 (mt) cc_final: 0.7603 (mt) REVERT: F 510 GLU cc_start: 0.7470 (tt0) cc_final: 0.7122 (tt0) REVERT: F 530 GLU cc_start: 0.8313 (pm20) cc_final: 0.6914 (pm20) outliers start: 49 outliers final: 35 residues processed: 364 average time/residue: 0.2781 time to fit residues: 140.9114 Evaluate side-chains 366 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 328 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 534 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 10 optimal weight: 0.0270 chunk 156 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN C 312 GLN ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 GLN ** F 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130159 restraints weight = 18008.877| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.94 r_work: 0.3605 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13976 Z= 0.161 Angle : 0.672 18.964 19017 Z= 0.306 Chirality : 0.044 0.170 2144 Planarity : 0.005 0.048 2430 Dihedral : 7.340 87.089 1927 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.36 % Allowed : 16.13 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.46 (0.20), residues: 1728 helix: 0.21 (0.18), residues: 843 sheet: -0.33 (0.41), residues: 180 loop : -0.79 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.007 0.001 HIS F 133 PHE 0.013 0.001 PHE A 109 TYR 0.013 0.001 TYR C 249 ARG 0.007 0.000 ARG F 310 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 653) hydrogen bonds : angle 4.96097 ( 1860) metal coordination : bond 0.01130 ( 8) metal coordination : angle 8.22053 ( 24) SS BOND : bond 0.00541 ( 1) SS BOND : angle 1.05537 ( 2) covalent geometry : bond 0.00381 (13967) covalent geometry : angle 0.60553 (18991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 330 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6673 (mmm) cc_final: 0.6443 (mmm) REVERT: A 248 MET cc_start: 0.6757 (ppp) cc_final: 0.6527 (ppp) REVERT: A 303 TYR cc_start: 0.8440 (m-80) cc_final: 0.8009 (m-80) REVERT: B 77 MET cc_start: 0.7219 (mmt) cc_final: 0.6680 (mmt) REVERT: B 168 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6653 (mm) REVERT: B 210 ASN cc_start: 0.8721 (m110) cc_final: 0.8375 (m-40) REVERT: B 239 PHE cc_start: 0.7064 (t80) cc_final: 0.6489 (t80) REVERT: C 24 ASP cc_start: 0.7942 (t0) cc_final: 0.7706 (t0) REVERT: C 26 ILE cc_start: 0.8570 (pt) cc_final: 0.8355 (pt) REVERT: C 32 GLN cc_start: 0.7344 (pm20) cc_final: 0.7087 (pm20) REVERT: C 41 GLU cc_start: 0.6951 (tt0) cc_final: 0.6689 (tt0) REVERT: C 64 MET cc_start: 0.7427 (mpp) cc_final: 0.7050 (mpp) REVERT: C 69 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7706 (mt-10) REVERT: C 80 GLU cc_start: 0.7033 (tp30) cc_final: 0.6831 (tp30) REVERT: C 129 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7220 (tm-30) REVERT: C 168 ILE cc_start: 0.8113 (mt) cc_final: 0.7878 (mp) REVERT: C 198 GLU cc_start: 0.6740 (tt0) cc_final: 0.6471 (tt0) REVERT: C 205 MET cc_start: 0.8152 (ttt) cc_final: 0.7923 (ttt) REVERT: C 287 ASN cc_start: 0.8202 (t160) cc_final: 0.7611 (m-40) REVERT: D 145 MET cc_start: 0.7395 (mtm) cc_final: 0.7127 (mtp) REVERT: D 152 THR cc_start: 0.8091 (m) cc_final: 0.7883 (m) REVERT: D 314 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7816 (mmmm) REVERT: F 35 SER cc_start: 0.8818 (t) cc_final: 0.8550 (p) REVERT: F 36 GLU cc_start: 0.7806 (tp30) cc_final: 0.7515 (tp30) REVERT: F 74 VAL cc_start: 0.7766 (t) cc_final: 0.7435 (m) REVERT: F 87 ASP cc_start: 0.8227 (t0) cc_final: 0.7894 (t0) REVERT: F 108 LYS cc_start: 0.7510 (tptp) cc_final: 0.7247 (tptp) REVERT: F 112 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7116 (mm-30) REVERT: F 135 VAL cc_start: 0.7279 (t) cc_final: 0.7065 (p) REVERT: F 146 MET cc_start: 0.6491 (tpt) cc_final: 0.6237 (tpp) REVERT: F 156 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7831 (ptmt) REVERT: F 254 TYR cc_start: 0.8446 (t80) cc_final: 0.7980 (t80) REVERT: F 276 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.6025 (mpp) REVERT: F 297 TYR cc_start: 0.7116 (m-80) cc_final: 0.6780 (m-10) REVERT: F 354 TYR cc_start: 0.6914 (t80) cc_final: 0.6643 (t80) REVERT: F 375 ASP cc_start: 0.7317 (p0) cc_final: 0.7024 (p0) REVERT: F 470 LEU cc_start: 0.7886 (mt) cc_final: 0.7611 (mt) REVERT: F 510 GLU cc_start: 0.7512 (tt0) cc_final: 0.7183 (tt0) REVERT: F 522 ASP cc_start: 0.7302 (t0) cc_final: 0.7005 (t0) REVERT: F 530 GLU cc_start: 0.8517 (pm20) cc_final: 0.7365 (pm20) outliers start: 49 outliers final: 36 residues processed: 357 average time/residue: 0.2841 time to fit residues: 141.8003 Evaluate side-chains 369 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 331 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 534 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 135 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN C 312 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 GLN ** F 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129060 restraints weight = 17985.841| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.95 r_work: 0.3585 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13976 Z= 0.219 Angle : 0.719 20.593 19017 Z= 0.327 Chirality : 0.046 0.173 2144 Planarity : 0.005 0.052 2430 Dihedral : 7.523 88.121 1927 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.43 % Allowed : 16.47 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.61 (0.20), residues: 1728 helix: 0.10 (0.18), residues: 840 sheet: -0.35 (0.41), residues: 180 loop : -0.91 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 293 HIS 0.009 0.001 HIS F 528 PHE 0.019 0.002 PHE D 162 TYR 0.013 0.002 TYR C 28 ARG 0.010 0.001 ARG F 310 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 653) hydrogen bonds : angle 5.03721 ( 1860) metal coordination : bond 0.01546 ( 8) metal coordination : angle 8.73097 ( 24) SS BOND : bond 0.00943 ( 1) SS BOND : angle 1.06043 ( 2) covalent geometry : bond 0.00521 (13967) covalent geometry : angle 0.64935 (18991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6673 (mmm) cc_final: 0.6439 (mmm) REVERT: A 248 MET cc_start: 0.6674 (ppp) cc_final: 0.6458 (ppp) REVERT: A 303 TYR cc_start: 0.8536 (m-80) cc_final: 0.8119 (m-80) REVERT: B 77 MET cc_start: 0.7236 (mmt) cc_final: 0.6683 (mmt) REVERT: B 168 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6688 (mm) REVERT: B 210 ASN cc_start: 0.8700 (m110) cc_final: 0.8357 (m-40) REVERT: B 239 PHE cc_start: 0.7112 (t80) cc_final: 0.6558 (t80) REVERT: C 24 ASP cc_start: 0.7938 (t0) cc_final: 0.7706 (t0) REVERT: C 26 ILE cc_start: 0.8585 (pt) cc_final: 0.8358 (pt) REVERT: C 32 GLN cc_start: 0.7338 (pm20) cc_final: 0.7058 (pm20) REVERT: C 41 GLU cc_start: 0.6962 (tt0) cc_final: 0.6692 (tt0) REVERT: C 64 MET cc_start: 0.7462 (mpp) cc_final: 0.7050 (mpp) REVERT: C 80 GLU cc_start: 0.7073 (tp30) cc_final: 0.6862 (tp30) REVERT: C 129 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 130 ARG cc_start: 0.7513 (ttm170) cc_final: 0.7201 (ttm170) REVERT: C 198 GLU cc_start: 0.6784 (tt0) cc_final: 0.6523 (tt0) REVERT: C 287 ASN cc_start: 0.8240 (t160) cc_final: 0.7663 (m-40) REVERT: D 145 MET cc_start: 0.7417 (mtm) cc_final: 0.7148 (mtp) REVERT: D 314 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7803 (mmmm) REVERT: F 35 SER cc_start: 0.8818 (t) cc_final: 0.8549 (p) REVERT: F 36 GLU cc_start: 0.7902 (tp30) cc_final: 0.7643 (tp30) REVERT: F 74 VAL cc_start: 0.7855 (t) cc_final: 0.7538 (m) REVERT: F 83 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6756 (tp30) REVERT: F 87 ASP cc_start: 0.8223 (t0) cc_final: 0.7905 (t0) REVERT: F 108 LYS cc_start: 0.7486 (tptp) cc_final: 0.7231 (tptp) REVERT: F 112 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7050 (mp0) REVERT: F 135 VAL cc_start: 0.7298 (t) cc_final: 0.7067 (p) REVERT: F 146 MET cc_start: 0.6609 (tpt) cc_final: 0.6340 (tpp) REVERT: F 156 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7760 (ptmm) REVERT: F 276 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.6030 (mpp) REVERT: F 297 TYR cc_start: 0.7164 (m-80) cc_final: 0.6827 (m-10) REVERT: F 354 TYR cc_start: 0.6939 (t80) cc_final: 0.6626 (t80) REVERT: F 375 ASP cc_start: 0.7352 (p0) cc_final: 0.7056 (p0) REVERT: F 388 ASN cc_start: 0.6833 (t0) cc_final: 0.6625 (t0) REVERT: F 470 LEU cc_start: 0.7921 (mt) cc_final: 0.7653 (mt) REVERT: F 510 GLU cc_start: 0.7554 (tt0) cc_final: 0.7270 (tt0) REVERT: F 522 ASP cc_start: 0.7375 (t0) cc_final: 0.7077 (t0) outliers start: 50 outliers final: 40 residues processed: 362 average time/residue: 0.3052 time to fit residues: 155.4012 Evaluate side-chains 370 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 534 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 39 optimal weight: 0.5980 chunk 135 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 116 optimal weight: 0.0870 chunk 107 optimal weight: 0.0270 chunk 162 optimal weight: 0.5980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN C 312 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132154 restraints weight = 17784.702| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.93 r_work: 0.3631 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13976 Z= 0.118 Angle : 0.641 14.059 19017 Z= 0.297 Chirality : 0.042 0.184 2144 Planarity : 0.005 0.050 2430 Dihedral : 7.237 89.934 1927 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.92 % Allowed : 18.53 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.26 (0.20), residues: 1728 helix: 0.40 (0.18), residues: 840 sheet: 0.02 (0.43), residues: 170 loop : -0.80 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 293 HIS 0.006 0.001 HIS F 528 PHE 0.012 0.001 PHE B 26 TYR 0.014 0.001 TYR C 249 ARG 0.010 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 653) hydrogen bonds : angle 4.84924 ( 1860) metal coordination : bond 0.00655 ( 8) metal coordination : angle 7.10849 ( 24) SS BOND : bond 0.00168 ( 1) SS BOND : angle 1.05733 ( 2) covalent geometry : bond 0.00268 (13967) covalent geometry : angle 0.58967 (18991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 331 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6626 (mmm) cc_final: 0.6376 (mmm) REVERT: A 185 MET cc_start: 0.7893 (tpp) cc_final: 0.7384 (tpp) REVERT: A 248 MET cc_start: 0.6860 (ppp) cc_final: 0.6655 (ppp) REVERT: A 303 TYR cc_start: 0.8465 (m-80) cc_final: 0.7809 (m-80) REVERT: B 77 MET cc_start: 0.7248 (mmt) cc_final: 0.6497 (mmt) REVERT: B 168 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6535 (mm) REVERT: B 210 ASN cc_start: 0.8718 (m110) cc_final: 0.8381 (m-40) REVERT: C 24 ASP cc_start: 0.7880 (t0) cc_final: 0.7675 (t0) REVERT: C 32 GLN cc_start: 0.7259 (pm20) cc_final: 0.7035 (pm20) REVERT: C 41 GLU cc_start: 0.6887 (tt0) cc_final: 0.6580 (tt0) REVERT: C 64 MET cc_start: 0.7416 (mpp) cc_final: 0.6937 (mpp) REVERT: C 69 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7733 (mt-10) REVERT: C 129 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7062 (tm-30) REVERT: C 198 GLU cc_start: 0.6700 (tt0) cc_final: 0.6447 (tt0) REVERT: C 200 GLN cc_start: 0.7493 (tm-30) cc_final: 0.7288 (tt0) REVERT: C 296 ARG cc_start: 0.6942 (mtp180) cc_final: 0.6626 (ttp-170) REVERT: D 145 MET cc_start: 0.7290 (mtm) cc_final: 0.7022 (mtp) REVERT: D 314 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7746 (mmmm) REVERT: F 35 SER cc_start: 0.8843 (t) cc_final: 0.8596 (p) REVERT: F 36 GLU cc_start: 0.7814 (tp30) cc_final: 0.7529 (tp30) REVERT: F 74 VAL cc_start: 0.7791 (t) cc_final: 0.7461 (m) REVERT: F 83 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6707 (tp30) REVERT: F 87 ASP cc_start: 0.8195 (t0) cc_final: 0.7859 (t0) REVERT: F 108 LYS cc_start: 0.7514 (tptp) cc_final: 0.7252 (tptp) REVERT: F 135 VAL cc_start: 0.7209 (t) cc_final: 0.6990 (p) REVERT: F 254 TYR cc_start: 0.8424 (t80) cc_final: 0.7870 (t80) REVERT: F 375 ASP cc_start: 0.7313 (p0) cc_final: 0.6989 (p0) REVERT: F 470 LEU cc_start: 0.7902 (mt) cc_final: 0.7641 (mt) outliers start: 28 outliers final: 19 residues processed: 350 average time/residue: 0.2837 time to fit residues: 139.3125 Evaluate side-chains 344 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 324 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain F residue 534 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 12 optimal weight: 0.0060 chunk 115 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 23 optimal weight: 0.0970 chunk 100 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 overall best weight: 0.1872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.146976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132608 restraints weight = 17599.392| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.91 r_work: 0.3635 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13976 Z= 0.119 Angle : 0.638 13.255 19017 Z= 0.297 Chirality : 0.042 0.181 2144 Planarity : 0.005 0.048 2430 Dihedral : 7.080 94.035 1926 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.58 % Allowed : 19.01 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.12 (0.20), residues: 1728 helix: 0.50 (0.18), residues: 845 sheet: 0.17 (0.43), residues: 170 loop : -0.76 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 293 HIS 0.008 0.001 HIS F 528 PHE 0.012 0.001 PHE C 110 TYR 0.013 0.001 TYR F 354 ARG 0.009 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 653) hydrogen bonds : angle 4.84286 ( 1860) metal coordination : bond 0.00594 ( 8) metal coordination : angle 6.42322 ( 24) SS BOND : bond 0.00144 ( 1) SS BOND : angle 1.55620 ( 2) covalent geometry : bond 0.00276 (13967) covalent geometry : angle 0.59546 (18991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6616 (mmm) cc_final: 0.6331 (mmm) REVERT: A 248 MET cc_start: 0.6886 (ppp) cc_final: 0.6678 (ppp) REVERT: A 303 TYR cc_start: 0.8298 (m-80) cc_final: 0.8044 (m-80) REVERT: B 77 MET cc_start: 0.7218 (mmt) cc_final: 0.6469 (mmt) REVERT: B 210 ASN cc_start: 0.8730 (m110) cc_final: 0.8393 (m-40) REVERT: B 239 PHE cc_start: 0.6956 (t80) cc_final: 0.6570 (t80) REVERT: C 32 GLN cc_start: 0.7258 (pm20) cc_final: 0.7024 (pm20) REVERT: C 41 GLU cc_start: 0.6892 (tt0) cc_final: 0.6628 (tt0) REVERT: C 64 MET cc_start: 0.7404 (mpp) cc_final: 0.6960 (mpp) REVERT: C 69 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 129 GLN cc_start: 0.7414 (tm-30) cc_final: 0.7014 (tm-30) REVERT: C 223 LYS cc_start: 0.8080 (tttt) cc_final: 0.7761 (ttpp) REVERT: D 145 MET cc_start: 0.7304 (mtm) cc_final: 0.7050 (mtp) REVERT: D 314 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7754 (mmmm) REVERT: F 35 SER cc_start: 0.8854 (t) cc_final: 0.8612 (p) REVERT: F 36 GLU cc_start: 0.7830 (tp30) cc_final: 0.7549 (tp30) REVERT: F 42 PHE cc_start: 0.7801 (m-10) cc_final: 0.7424 (m-10) REVERT: F 74 VAL cc_start: 0.7779 (t) cc_final: 0.7451 (m) REVERT: F 83 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6748 (tp30) REVERT: F 87 ASP cc_start: 0.8193 (t0) cc_final: 0.7858 (t0) REVERT: F 108 LYS cc_start: 0.7426 (tptp) cc_final: 0.7206 (tptp) REVERT: F 135 VAL cc_start: 0.7249 (t) cc_final: 0.7023 (p) REVERT: F 156 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7715 (ptmt) REVERT: F 254 TYR cc_start: 0.8398 (t80) cc_final: 0.8013 (t80) REVERT: F 470 LEU cc_start: 0.7892 (mt) cc_final: 0.7622 (mt) outliers start: 23 outliers final: 20 residues processed: 345 average time/residue: 0.2894 time to fit residues: 138.8216 Evaluate side-chains 341 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain F residue 534 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 32 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 152 optimal weight: 0.0770 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 131 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 12 optimal weight: 0.0060 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 111 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.133390 restraints weight = 17707.896| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.93 r_work: 0.3645 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13976 Z= 0.115 Angle : 0.639 12.518 19017 Z= 0.299 Chirality : 0.043 0.382 2144 Planarity : 0.004 0.048 2430 Dihedral : 6.945 98.540 1926 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 19.49 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.04 (0.21), residues: 1728 helix: 0.58 (0.18), residues: 853 sheet: 0.20 (0.43), residues: 170 loop : -0.72 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.006 0.001 HIS F 528 PHE 0.021 0.001 PHE F 107 TYR 0.014 0.001 TYR F 294 ARG 0.008 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 653) hydrogen bonds : angle 4.85591 ( 1860) metal coordination : bond 0.00550 ( 8) metal coordination : angle 6.03999 ( 24) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.50219 ( 2) covalent geometry : bond 0.00264 (13967) covalent geometry : angle 0.60244 (18991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 314 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6573 (mmm) cc_final: 0.6276 (mmm) REVERT: A 185 MET cc_start: 0.7908 (tpp) cc_final: 0.7379 (tpp) REVERT: A 205 MET cc_start: 0.7139 (tpp) cc_final: 0.6811 (tpt) REVERT: B 77 MET cc_start: 0.7193 (mmt) cc_final: 0.6440 (mmt) REVERT: B 210 ASN cc_start: 0.8739 (m110) cc_final: 0.8402 (m-40) REVERT: B 239 PHE cc_start: 0.6916 (t80) cc_final: 0.6707 (t80) REVERT: C 32 GLN cc_start: 0.7262 (pm20) cc_final: 0.7039 (pm20) REVERT: C 41 GLU cc_start: 0.6973 (tt0) cc_final: 0.6574 (tp30) REVERT: C 64 MET cc_start: 0.7387 (mpp) cc_final: 0.7025 (mpp) REVERT: C 69 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7684 (mt-10) REVERT: C 129 GLN cc_start: 0.7345 (tm-30) cc_final: 0.6919 (tm-30) REVERT: D 145 MET cc_start: 0.7319 (mtm) cc_final: 0.7081 (mtp) REVERT: D 193 ASP cc_start: 0.5805 (p0) cc_final: 0.5598 (p0) REVERT: D 314 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7727 (mmmm) REVERT: F 35 SER cc_start: 0.8857 (t) cc_final: 0.8621 (p) REVERT: F 36 GLU cc_start: 0.7839 (tp30) cc_final: 0.7583 (tp30) REVERT: F 42 PHE cc_start: 0.7812 (m-10) cc_final: 0.7502 (m-10) REVERT: F 74 VAL cc_start: 0.7767 (t) cc_final: 0.7429 (m) REVERT: F 83 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6767 (tp30) REVERT: F 87 ASP cc_start: 0.8189 (t0) cc_final: 0.7850 (t0) REVERT: F 108 LYS cc_start: 0.7339 (tptp) cc_final: 0.6961 (tptp) REVERT: F 135 VAL cc_start: 0.7261 (t) cc_final: 0.7059 (p) REVERT: F 156 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7704 (ptmt) REVERT: F 189 GLU cc_start: 0.7161 (tp30) cc_final: 0.6620 (mt-10) REVERT: F 254 TYR cc_start: 0.8346 (t80) cc_final: 0.7647 (t80) REVERT: F 470 LEU cc_start: 0.7876 (mt) cc_final: 0.7607 (mt) outliers start: 22 outliers final: 18 residues processed: 327 average time/residue: 0.2972 time to fit residues: 135.5540 Evaluate side-chains 331 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 313 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain F residue 534 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 144 optimal weight: 0.6980 chunk 143 optimal weight: 0.1980 chunk 133 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 165 optimal weight: 0.0870 chunk 64 optimal weight: 0.0670 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 111 GLN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133178 restraints weight = 17809.966| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.93 r_work: 0.3645 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.365 13976 Z= 0.266 Angle : 0.859 65.898 19017 Z= 0.480 Chirality : 0.050 1.143 2144 Planarity : 0.007 0.259 2430 Dihedral : 6.947 98.526 1926 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 19.90 % Favored : 78.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.04 (0.21), residues: 1728 helix: 0.57 (0.18), residues: 853 sheet: 0.21 (0.43), residues: 170 loop : -0.73 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 293 HIS 0.005 0.001 HIS F 528 PHE 0.023 0.001 PHE F 107 TYR 0.012 0.001 TYR C 249 ARG 0.006 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 653) hydrogen bonds : angle 4.84699 ( 1860) metal coordination : bond 0.00578 ( 8) metal coordination : angle 6.02786 ( 24) SS BOND : bond 0.00144 ( 1) SS BOND : angle 1.48661 ( 2) covalent geometry : bond 0.00584 (13967) covalent geometry : angle 0.83258 (18991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6911.18 seconds wall clock time: 120 minutes 11.66 seconds (7211.66 seconds total)