Starting phenix.real_space_refine on Thu Sep 18 03:41:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1z_39741/09_2025/8z1z_39741_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1z_39741/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z1z_39741/09_2025/8z1z_39741_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1z_39741/09_2025/8z1z_39741_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z1z_39741/09_2025/8z1z_39741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1z_39741/09_2025/8z1z_39741.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.12, per 1000 atoms: 0.23 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: 0.92 Conformation dependent library (CDL) restraints added in 484.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.54 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: 2.20 Time building geometry restraints manager: 1.30 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: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.110 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG F 253 TYR 0.157 0.023 TYR A 141 PHE 0.108 0.012 PHE F 182 TRP 0.157 0.019 TRP A 148 HIS 0.013 0.003 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.02703 (13967) covalent geometry : angle 2.37814 (18991) SS BOND : bond 0.05232 ( 1) SS BOND : angle 0.36727 ( 2) hydrogen bonds : bond 0.19683 ( 653) hydrogen bonds : angle 8.05648 ( 1860) metal coordination : bond 0.21566 ( 8) metal coordination : angle 9.32460 ( 24) *********************** 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 : 0.463 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: 0.7694 (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: 0.7125 (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: 0.6621 (m-10) REVERT: A 257 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7186 (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: 0.7765 (p) REVERT: C 66 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7531 (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: 0.5268 (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: 0.5851 (tp30) REVERT: C 82 GLU cc_start: 0.6864 (tt0) cc_final: 0.6567 (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: 0.6696 (tp40) REVERT: C 127 ARG cc_start: 0.7294 (mtp180) cc_final: 0.6948 (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: 0.7477 (m-30) REVERT: C 168 ILE cc_start: 0.7465 (mt) cc_final: 0.7141 (mp) REVERT: C 175 LEU cc_start: 0.8128 (tt) cc_final: 0.7790 (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: 0.7012 (mt-10) REVERT: C 234 GLU cc_start: 0.7724 (tt0) cc_final: 0.7422 (tt0) REVERT: C 313 SER cc_start: 0.7827 (p) cc_final: 0.7604 (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: 0.5235 (pmm) REVERT: D 36 LYS cc_start: 0.7616 (mmtp) cc_final: 0.7386 (mmtp) REVERT: D 46 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6894 (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: 0.7224 (pp30) REVERT: D 314 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7157 (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: 0.7879 (p) REVERT: F 36 GLU cc_start: 0.7205 (tp30) cc_final: 0.6445 (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: 0.5825 (tp30) REVERT: F 156 LYS cc_start: 0.7465 (mtmt) cc_final: 0.6834 (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: 0.7401 (p) 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: 0.5618 (mmt) REVERT: F 347 ASP cc_start: 0.7532 (p0) cc_final: 0.7208 (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: 0.5714 (t0) REVERT: F 395 MET cc_start: 0.6613 (mtp) cc_final: 0.6133 (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: 0.1355 time to fit residues: 78.0196 Evaluate side-chains 358 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 347 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 189 ASN B 260 GLN C 179 GLN D 82 GLN D 89 HIS D 154 HIS D 187 GLN F 62 ASN ** F 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 269 ASN F 298 ASN F 397 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131814 restraints weight = 17957.418| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.93 r_work: 0.3626 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13976 Z= 0.168 Angle : 0.742 24.415 19017 Z= 0.354 Chirality : 0.046 0.211 2144 Planarity : 0.005 0.047 2430 Dihedral : 8.189 99.035 1946 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.58 % Allowed : 9.61 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.19), residues: 1728 helix: -0.32 (0.17), residues: 831 sheet: -0.40 (0.39), residues: 178 loop : -0.70 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 93 TYR 0.017 0.002 TYR C 249 PHE 0.016 0.002 PHE A 92 TRP 0.022 0.002 TRP A 293 HIS 0.014 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00376 (13967) covalent geometry : angle 0.67374 (18991) SS BOND : bond 0.00433 ( 1) SS BOND : angle 1.43827 ( 2) hydrogen bonds : bond 0.04998 ( 653) hydrogen bonds : angle 5.57156 ( 1860) metal coordination : bond 0.01332 ( 8) metal coordination : angle 8.76603 ( 24) *********************** 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 363 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 340 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8011 (mmm) cc_final: 0.7635 (tpp) REVERT: A 248 MET cc_start: 0.6837 (ppp) cc_final: 0.6571 (ppp) REVERT: A 260 MET cc_start: 0.6867 (mmt) cc_final: 0.6548 (mmm) REVERT: A 307 GLN cc_start: 0.6620 (mt0) cc_final: 0.6399 (mt0) REVERT: B 77 MET cc_start: 0.6959 (mmt) cc_final: 0.6576 (mmt) REVERT: B 168 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6741 (mt) REVERT: B 210 ASN cc_start: 0.8657 (m110) cc_final: 0.8345 (m-40) REVERT: C 32 GLN cc_start: 0.7374 (pm20) cc_final: 0.7033 (pm20) REVERT: C 41 GLU cc_start: 0.7018 (tt0) cc_final: 0.6621 (tt0) REVERT: C 64 MET cc_start: 0.7412 (mpp) cc_final: 0.7103 (mpp) REVERT: C 129 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7309 (tm-30) REVERT: C 168 ILE cc_start: 0.8093 (mt) cc_final: 0.7815 (mp) REVERT: C 198 GLU cc_start: 0.6634 (tt0) cc_final: 0.6385 (tt0) REVERT: D 28 MET cc_start: 0.5858 (pmm) cc_final: 0.5461 (pmm) REVERT: D 41 VAL cc_start: 0.8331 (t) cc_final: 0.8122 (m) REVERT: D 314 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7972 (ttmm) REVERT: F 35 SER cc_start: 0.8743 (t) cc_final: 0.8535 (p) REVERT: F 42 PHE cc_start: 0.7866 (m-80) cc_final: 0.7648 (m-80) REVERT: F 67 PHE cc_start: 0.7507 (m-80) cc_final: 0.7264 (m-80) REVERT: F 87 ASP cc_start: 0.8053 (t0) cc_final: 0.7847 (t0) REVERT: F 135 VAL cc_start: 0.7260 (t) cc_final: 0.6982 (p) REVERT: F 261 GLU cc_start: 0.7224 (tt0) cc_final: 0.6840 (tt0) REVERT: F 265 MET cc_start: 0.7921 (ttt) cc_final: 0.7689 (ttp) REVERT: F 276 MET cc_start: 0.6840 (mtp) cc_final: 0.6623 (mtp) REVERT: F 388 ASN cc_start: 0.6846 (t0) cc_final: 0.6590 (t0) REVERT: F 470 LEU cc_start: 0.7979 (mt) cc_final: 0.7740 (mt) REVERT: F 528 HIS cc_start: 0.8420 (m-70) cc_final: 0.8086 (m-70) outliers start: 23 outliers final: 15 residues processed: 355 average time/residue: 0.1470 time to fit residues: 72.4505 Evaluate side-chains 338 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 271 VAL 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 164 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 F 397 GLN F 527 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129855 restraints weight = 17964.006| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.93 r_work: 0.3604 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13976 Z= 0.194 Angle : 0.719 23.818 19017 Z= 0.335 Chirality : 0.046 0.279 2144 Planarity : 0.005 0.048 2430 Dihedral : 7.761 91.009 1931 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.88 % Allowed : 12.56 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1728 helix: -0.12 (0.17), residues: 851 sheet: -0.42 (0.39), residues: 187 loop : -0.82 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 298 TYR 0.016 0.002 TYR C 28 PHE 0.020 0.002 PHE A 184 TRP 0.014 0.002 TRP A 293 HIS 0.006 0.001 HIS F 505 Details of bonding type rmsd covalent geometry : bond 0.00463 (13967) covalent geometry : angle 0.64908 (18991) SS BOND : bond 0.00759 ( 1) SS BOND : angle 1.41079 ( 2) hydrogen bonds : bond 0.04738 ( 653) hydrogen bonds : angle 5.20746 ( 1860) metal coordination : bond 0.01311 ( 8) metal coordination : angle 8.70179 ( 24) *********************** 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: 42 poor density : 336 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LEU cc_start: 0.7638 (mt) cc_final: 0.7319 (mp) REVERT: A 189 THR cc_start: 0.8414 (p) cc_final: 0.8198 (p) REVERT: A 248 MET cc_start: 0.6772 (ppp) cc_final: 0.6470 (ppp) REVERT: A 303 TYR cc_start: 0.8405 (m-80) cc_final: 0.7842 (m-80) REVERT: B 26 PHE cc_start: 0.7907 (t80) cc_final: 0.7675 (t80) REVERT: B 77 MET cc_start: 0.7169 (mmt) cc_final: 0.6598 (mmt) REVERT: B 168 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6829 (mm) REVERT: B 210 ASN cc_start: 0.8684 (m110) cc_final: 0.8351 (m-40) REVERT: B 239 PHE cc_start: 0.6948 (t80) cc_final: 0.6416 (t80) REVERT: C 32 GLN cc_start: 0.7351 (pm20) cc_final: 0.7028 (pm20) REVERT: C 41 GLU cc_start: 0.6880 (tt0) cc_final: 0.6565 (tt0) REVERT: C 64 MET cc_start: 0.7418 (mpp) cc_final: 0.7085 (mpp) REVERT: C 80 GLU cc_start: 0.7036 (tp30) cc_final: 0.6804 (tp30) REVERT: C 129 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 168 ILE cc_start: 0.8111 (mt) cc_final: 0.7864 (mp) REVERT: C 198 GLU cc_start: 0.6695 (tt0) cc_final: 0.6457 (tt0) REVERT: D 314 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7980 (ttmm) REVERT: F 35 SER cc_start: 0.8785 (t) cc_final: 0.8546 (p) REVERT: F 36 GLU cc_start: 0.7764 (tp30) cc_final: 0.7281 (tp30) REVERT: F 87 ASP cc_start: 0.8112 (t0) cc_final: 0.7803 (t0) REVERT: F 135 VAL cc_start: 0.7357 (t) cc_final: 0.7104 (p) REVERT: F 146 MET cc_start: 0.6307 (tpt) cc_final: 0.6057 (tpt) REVERT: F 254 TYR cc_start: 0.8456 (t80) cc_final: 0.8034 (t80) REVERT: F 265 MET cc_start: 0.7910 (ttt) cc_final: 0.7703 (ttp) REVERT: F 297 TYR cc_start: 0.7195 (m-80) cc_final: 0.6914 (m-80) REVERT: F 388 ASN cc_start: 0.6940 (t0) cc_final: 0.6720 (t0) REVERT: F 392 MET cc_start: 0.7313 (mtp) cc_final: 0.7047 (mtt) REVERT: F 458 ASN cc_start: 0.6971 (t0) cc_final: 0.6641 (t0) REVERT: F 470 LEU cc_start: 0.7871 (mt) cc_final: 0.7599 (mt) REVERT: F 530 GLU cc_start: 0.7512 (pm20) cc_final: 0.5981 (pm20) outliers start: 42 outliers final: 27 residues processed: 356 average time/residue: 0.1424 time to fit residues: 70.4384 Evaluate side-chains 355 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 327 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 115 ILE 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 78 ILE 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 235 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 120 optimal weight: 0.1980 chunk 52 optimal weight: 0.0170 chunk 39 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 92 optimal weight: 0.6980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN D 160 HIS F 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131283 restraints weight = 17933.964| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.93 r_work: 0.3625 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13976 Z= 0.133 Angle : 0.656 19.008 19017 Z= 0.300 Chirality : 0.043 0.180 2144 Planarity : 0.005 0.044 2430 Dihedral : 7.423 85.015 1929 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.68 % Allowed : 14.76 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.20), residues: 1728 helix: 0.23 (0.18), residues: 846 sheet: -0.43 (0.40), residues: 178 loop : -0.72 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 310 TYR 0.013 0.001 TYR C 249 PHE 0.013 0.001 PHE B 44 TRP 0.017 0.001 TRP A 293 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00307 (13967) covalent geometry : angle 0.59420 (18991) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.14030 ( 2) hydrogen bonds : bond 0.04057 ( 653) hydrogen bonds : angle 4.96650 ( 1860) metal coordination : bond 0.00797 ( 8) metal coordination : angle 7.81018 ( 24) *********************** 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 377 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 0.519 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 29 MET cc_start: 0.6709 (mmm) cc_final: 0.6500 (mmm) REVERT: A 185 MET cc_start: 0.7867 (tpp) cc_final: 0.7503 (tpp) REVERT: A 248 MET cc_start: 0.6770 (ppp) cc_final: 0.6545 (ppp) REVERT: A 303 TYR cc_start: 0.8411 (m-80) cc_final: 0.8147 (m-80) REVERT: B 26 PHE cc_start: 0.7862 (t80) cc_final: 0.7580 (t80) REVERT: B 77 MET cc_start: 0.7182 (mmt) cc_final: 0.6617 (mmt) REVERT: B 168 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6732 (mm) REVERT: B 210 ASN cc_start: 0.8708 (m110) cc_final: 0.8341 (m-40) REVERT: B 239 PHE cc_start: 0.6968 (t80) cc_final: 0.6385 (t80) REVERT: C 32 GLN cc_start: 0.7344 (pm20) cc_final: 0.7053 (pm20) REVERT: C 41 GLU cc_start: 0.6894 (tt0) cc_final: 0.6657 (tt0) REVERT: C 64 MET cc_start: 0.7394 (mpp) cc_final: 0.6895 (mpp) REVERT: C 69 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 80 GLU cc_start: 0.7058 (tp30) cc_final: 0.6833 (tp30) REVERT: C 129 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 168 ILE cc_start: 0.8118 (mt) cc_final: 0.7864 (mp) REVERT: C 198 GLU cc_start: 0.6666 (tt0) cc_final: 0.6433 (tt0) REVERT: D 145 MET cc_start: 0.7303 (mtm) cc_final: 0.7006 (mtp) REVERT: D 314 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7823 (mmmm) REVERT: F 35 SER cc_start: 0.8765 (t) cc_final: 0.8526 (p) REVERT: F 74 VAL cc_start: 0.7658 (t) cc_final: 0.7304 (m) REVERT: F 83 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6840 (mt-10) REVERT: F 87 ASP cc_start: 0.8182 (t0) cc_final: 0.7871 (t0) REVERT: F 112 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7095 (mm-30) REVERT: F 135 VAL cc_start: 0.7314 (t) cc_final: 0.7089 (p) REVERT: F 156 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7777 (ptmt) REVERT: F 189 GLU cc_start: 0.7200 (tp30) cc_final: 0.6525 (mt-10) REVERT: F 254 TYR cc_start: 0.8358 (t80) cc_final: 0.7828 (t80) REVERT: F 297 TYR cc_start: 0.7162 (m-80) cc_final: 0.6886 (m-10) REVERT: F 470 LEU cc_start: 0.7828 (mt) cc_final: 0.7569 (mt) REVERT: F 530 GLU cc_start: 0.7860 (pm20) cc_final: 0.6674 (pm20) outliers start: 39 outliers final: 22 residues processed: 359 average time/residue: 0.1429 time to fit residues: 71.5516 Evaluate side-chains 358 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 335 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 271 VAL Chi-restraints excluded: chain A residue 295 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 91 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 262 CYS Chi-restraints excluded: chain F residue 408 LYS Chi-restraints excluded: chain F residue 441 ASP 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 140 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 130 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 0.0970 chunk 48 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN F 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131709 restraints weight = 17966.517| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.93 r_work: 0.3633 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13976 Z= 0.126 Angle : 0.635 15.662 19017 Z= 0.294 Chirality : 0.043 0.184 2144 Planarity : 0.004 0.044 2430 Dihedral : 7.163 85.899 1927 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.20 % Allowed : 15.92 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1728 helix: 0.41 (0.18), residues: 844 sheet: -0.36 (0.41), residues: 176 loop : -0.65 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 310 TYR 0.012 0.001 TYR C 249 PHE 0.012 0.001 PHE B 44 TRP 0.015 0.001 TRP A 293 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00294 (13967) covalent geometry : angle 0.58382 (18991) SS BOND : bond 0.00303 ( 1) SS BOND : angle 1.15067 ( 2) hydrogen bonds : bond 0.03872 ( 653) hydrogen bonds : angle 4.86316 ( 1860) metal coordination : bond 0.00732 ( 8) metal coordination : angle 7.06201 ( 24) *********************** 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 375 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 343 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6670 (mmm) cc_final: 0.6448 (mmm) REVERT: A 248 MET cc_start: 0.6855 (ppp) cc_final: 0.6611 (ppp) REVERT: A 303 TYR cc_start: 0.8390 (m-80) cc_final: 0.7988 (m-80) REVERT: B 26 PHE cc_start: 0.7831 (t80) cc_final: 0.7520 (t80) REVERT: B 77 MET cc_start: 0.7225 (mmt) cc_final: 0.6692 (mmt) REVERT: B 168 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6676 (mm) REVERT: B 210 ASN cc_start: 0.8728 (m110) cc_final: 0.8357 (m-40) REVERT: B 239 PHE cc_start: 0.6961 (t80) cc_final: 0.6425 (t80) REVERT: C 26 ILE cc_start: 0.8577 (pt) cc_final: 0.8361 (pt) REVERT: C 32 GLN cc_start: 0.7317 (pm20) cc_final: 0.7072 (pm20) REVERT: C 41 GLU cc_start: 0.6891 (tt0) cc_final: 0.6652 (tt0) REVERT: C 64 MET cc_start: 0.7401 (mpp) cc_final: 0.6949 (mpp) REVERT: C 69 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7626 (mt-10) REVERT: C 80 GLU cc_start: 0.7032 (tp30) cc_final: 0.6811 (tp30) REVERT: C 129 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7113 (tm-30) REVERT: C 130 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7144 (ttm170) REVERT: C 168 ILE cc_start: 0.8104 (mt) cc_final: 0.7855 (mp) REVERT: C 198 GLU cc_start: 0.6714 (tt0) cc_final: 0.6473 (tt0) REVERT: C 200 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7376 (tt0) REVERT: C 234 GLU cc_start: 0.7673 (tt0) cc_final: 0.7421 (mt-10) REVERT: C 287 ASN cc_start: 0.8154 (t0) cc_final: 0.7454 (m-40) REVERT: D 145 MET cc_start: 0.7324 (mtm) cc_final: 0.7049 (mtp) REVERT: D 314 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7825 (mmmm) REVERT: F 35 SER cc_start: 0.8758 (t) cc_final: 0.8508 (p) REVERT: F 74 VAL cc_start: 0.7599 (t) cc_final: 0.7249 (m) REVERT: F 83 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6786 (mt-10) REVERT: F 87 ASP cc_start: 0.8162 (t0) cc_final: 0.7821 (t0) REVERT: F 135 VAL cc_start: 0.7309 (t) cc_final: 0.7093 (p) REVERT: F 156 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7753 (ptmt) REVERT: F 189 GLU cc_start: 0.7186 (tp30) cc_final: 0.6565 (mt-10) REVERT: F 254 TYR cc_start: 0.8380 (t80) cc_final: 0.7987 (t80) REVERT: F 297 TYR cc_start: 0.7127 (m-80) cc_final: 0.6802 (m-10) REVERT: F 354 TYR cc_start: 0.6814 (t80) cc_final: 0.6607 (t80) REVERT: F 388 ASN cc_start: 0.6830 (t0) cc_final: 0.6609 (t0) REVERT: F 470 LEU cc_start: 0.7865 (mt) cc_final: 0.7603 (mt) REVERT: F 522 ASP cc_start: 0.7109 (t0) cc_final: 0.6851 (t0) REVERT: F 530 GLU cc_start: 0.8065 (pm20) cc_final: 0.6792 (pm20) outliers start: 32 outliers final: 22 residues processed: 357 average time/residue: 0.1404 time to fit residues: 69.2385 Evaluate side-chains 363 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 340 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 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 107 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 102 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 84 ARG Chi-restraints excluded: chain C residue 217 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 223 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 309 LEU 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 28 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 312 GLN ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129929 restraints weight = 17944.983| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.94 r_work: 0.3602 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13976 Z= 0.185 Angle : 0.690 18.380 19017 Z= 0.313 Chirality : 0.044 0.174 2144 Planarity : 0.005 0.048 2430 Dihedral : 7.162 87.473 1924 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.61 % Allowed : 16.82 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1728 helix: 0.34 (0.18), residues: 843 sheet: -0.28 (0.41), residues: 180 loop : -0.75 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 298 TYR 0.016 0.002 TYR F 294 PHE 0.016 0.002 PHE B 44 TRP 0.009 0.001 TRP A 293 HIS 0.007 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00439 (13967) covalent geometry : angle 0.62718 (18991) SS BOND : bond 0.00739 ( 1) SS BOND : angle 1.33651 ( 2) hydrogen bonds : bond 0.04169 ( 653) hydrogen bonds : angle 4.96086 ( 1860) metal coordination : bond 0.01287 ( 8) metal coordination : angle 8.10006 ( 24) *********************** 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 374 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 336 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6630 (mmm) cc_final: 0.6378 (mmm) REVERT: A 185 MET cc_start: 0.7895 (tpp) cc_final: 0.7247 (tpp) REVERT: A 248 MET cc_start: 0.6803 (ppp) cc_final: 0.6556 (ppp) REVERT: A 303 TYR cc_start: 0.8441 (m-80) cc_final: 0.8045 (m-80) REVERT: B 77 MET cc_start: 0.7251 (mmt) cc_final: 0.6691 (mmt) REVERT: B 168 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6687 (mm) REVERT: B 210 ASN cc_start: 0.8725 (m110) cc_final: 0.8379 (m-40) REVERT: B 239 PHE cc_start: 0.7055 (t80) cc_final: 0.6503 (t80) REVERT: C 26 ILE cc_start: 0.8554 (pt) cc_final: 0.8338 (pt) REVERT: C 32 GLN cc_start: 0.7307 (pm20) cc_final: 0.7059 (pm20) REVERT: C 64 MET cc_start: 0.7412 (mpp) cc_final: 0.7062 (mpp) REVERT: C 80 GLU cc_start: 0.7043 (tp30) cc_final: 0.6840 (tp30) REVERT: C 129 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 168 ILE cc_start: 0.8099 (mt) cc_final: 0.7856 (mp) REVERT: C 198 GLU cc_start: 0.6723 (tt0) cc_final: 0.6462 (tt0) REVERT: C 234 GLU cc_start: 0.7718 (tt0) cc_final: 0.7445 (mt-10) REVERT: C 287 ASN cc_start: 0.8224 (t0) cc_final: 0.7459 (m-40) REVERT: D 314 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7828 (mmmm) REVERT: F 35 SER cc_start: 0.8872 (t) cc_final: 0.8607 (p) REVERT: F 36 GLU cc_start: 0.7782 (tp30) cc_final: 0.7492 (tp30) REVERT: F 74 VAL cc_start: 0.7782 (t) cc_final: 0.7450 (m) REVERT: F 87 ASP cc_start: 0.8175 (t0) cc_final: 0.7846 (t0) REVERT: F 135 VAL cc_start: 0.7302 (t) cc_final: 0.7096 (p) REVERT: F 156 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7795 (ptmt) REVERT: F 254 TYR cc_start: 0.8517 (t80) cc_final: 0.8226 (t80) REVERT: F 354 TYR cc_start: 0.6832 (t80) cc_final: 0.6569 (t80) REVERT: F 375 ASP cc_start: 0.7322 (p0) cc_final: 0.7010 (p0) REVERT: F 388 ASN cc_start: 0.6938 (t0) cc_final: 0.6668 (t0) REVERT: F 470 LEU cc_start: 0.7893 (mt) cc_final: 0.7618 (mt) REVERT: F 510 GLU cc_start: 0.7465 (tt0) cc_final: 0.7129 (tt0) REVERT: F 522 ASP cc_start: 0.7249 (t0) cc_final: 0.7019 (t0) REVERT: F 530 GLU cc_start: 0.8499 (pm20) cc_final: 0.7150 (pm20) outliers start: 38 outliers final: 28 residues processed: 354 average time/residue: 0.1326 time to fit residues: 66.0032 Evaluate side-chains 363 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 334 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE 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 261 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 102 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 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 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 F residue 262 CYS Chi-restraints excluded: chain F residue 408 LYS 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 97 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 158 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 214 ASN C 312 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 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 = 0.3894 r_free = 0.3894 target = 0.144713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130271 restraints weight = 17856.926| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.94 r_work: 0.3608 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3221 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= 0.166 Angle : 0.674 17.166 19017 Z= 0.307 Chirality : 0.044 0.185 2144 Planarity : 0.005 0.048 2430 Dihedral : 7.138 88.209 1924 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.61 % Allowed : 17.57 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.20), residues: 1728 helix: 0.38 (0.18), residues: 844 sheet: -0.25 (0.41), residues: 180 loop : -0.78 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 300 TYR 0.012 0.001 TYR C 249 PHE 0.013 0.001 PHE B 44 TRP 0.011 0.001 TRP A 293 HIS 0.007 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00396 (13967) covalent geometry : angle 0.61317 (18991) SS BOND : bond 0.00583 ( 1) SS BOND : angle 1.38327 ( 2) hydrogen bonds : bond 0.04034 ( 653) hydrogen bonds : angle 4.93212 ( 1860) metal coordination : bond 0.01100 ( 8) metal coordination : angle 7.91334 ( 24) *********************** 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 371 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 333 time to evaluate : 0.502 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: 0.6577 (mmm) cc_final: 0.6315 (mmm) REVERT: A 248 MET cc_start: 0.6839 (ppp) cc_final: 0.6608 (ppp) REVERT: A 303 TYR cc_start: 0.8490 (m-80) cc_final: 0.8036 (m-80) REVERT: B 77 MET cc_start: 0.7246 (mmt) cc_final: 0.6705 (mmt) REVERT: B 168 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6623 (mm) REVERT: B 210 ASN cc_start: 0.8707 (m110) cc_final: 0.8383 (m-40) REVERT: B 239 PHE cc_start: 0.7056 (t80) cc_final: 0.6482 (t80) REVERT: C 24 ASP cc_start: 0.7918 (t0) cc_final: 0.7695 (t0) REVERT: C 26 ILE cc_start: 0.8578 (pt) cc_final: 0.8360 (pt) REVERT: C 32 GLN cc_start: 0.7318 (pm20) cc_final: 0.7077 (pm20) REVERT: C 64 MET cc_start: 0.7397 (mpp) cc_final: 0.6861 (mpp) REVERT: C 69 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7739 (mt-10) REVERT: C 80 GLU cc_start: 0.7059 (tp30) cc_final: 0.6857 (tp30) REVERT: C 129 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7150 (tm-30) REVERT: C 198 GLU cc_start: 0.6727 (tt0) cc_final: 0.6463 (tt0) REVERT: C 234 GLU cc_start: 0.7701 (tt0) cc_final: 0.7410 (mt-10) REVERT: C 287 ASN cc_start: 0.8166 (t0) cc_final: 0.7364 (m-40) REVERT: D 314 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7823 (mmmm) REVERT: F 35 SER cc_start: 0.8880 (t) cc_final: 0.8622 (p) REVERT: F 36 GLU cc_start: 0.7810 (tp30) cc_final: 0.7514 (tp30) REVERT: F 42 PHE cc_start: 0.7810 (m-80) cc_final: 0.7432 (m-10) REVERT: F 54 ASP cc_start: 0.7614 (t0) cc_final: 0.7410 (t0) REVERT: F 74 VAL cc_start: 0.7815 (t) cc_final: 0.7485 (m) REVERT: F 83 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6863 (mt-10) REVERT: F 87 ASP cc_start: 0.8197 (t0) cc_final: 0.7878 (t0) REVERT: F 156 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7801 (ptmt) REVERT: F 254 TYR cc_start: 0.8515 (t80) cc_final: 0.8253 (t80) REVERT: F 375 ASP cc_start: 0.7343 (p0) cc_final: 0.7045 (p0) REVERT: F 388 ASN cc_start: 0.6945 (t0) cc_final: 0.6703 (t0) REVERT: F 470 LEU cc_start: 0.7888 (mt) cc_final: 0.7614 (mt) REVERT: F 510 GLU cc_start: 0.7471 (tt0) cc_final: 0.7202 (tt0) REVERT: F 522 ASP cc_start: 0.7270 (t0) cc_final: 0.7052 (t0) REVERT: F 530 GLU cc_start: 0.8681 (pm20) cc_final: 0.6820 (pm20) outliers start: 38 outliers final: 29 residues processed: 358 average time/residue: 0.1332 time to fit residues: 66.8695 Evaluate side-chains 361 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 331 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 155 LEU 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 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 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 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 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 408 LYS 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 74 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 167 optimal weight: 0.0770 chunk 82 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130743 restraints weight = 17782.581| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.92 r_work: 0.3614 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3342 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= 0.165 Angle : 0.680 16.309 19017 Z= 0.309 Chirality : 0.044 0.194 2144 Planarity : 0.005 0.048 2430 Dihedral : 7.151 90.421 1924 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.61 % Allowed : 17.64 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1728 helix: 0.38 (0.18), residues: 842 sheet: -0.26 (0.41), residues: 180 loop : -0.83 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 300 TYR 0.014 0.002 TYR F 354 PHE 0.025 0.001 PHE B 26 TRP 0.012 0.001 TRP A 293 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00395 (13967) covalent geometry : angle 0.62206 (18991) SS BOND : bond 0.00545 ( 1) SS BOND : angle 1.36517 ( 2) hydrogen bonds : bond 0.04009 ( 653) hydrogen bonds : angle 4.95024 ( 1860) metal coordination : bond 0.01141 ( 8) metal coordination : angle 7.72401 ( 24) *********************** 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 363 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 325 time to evaluate : 0.590 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: 0.6468 (mmm) cc_final: 0.6212 (mmm) REVERT: A 248 MET cc_start: 0.6855 (ppp) cc_final: 0.6642 (ppp) REVERT: A 303 TYR cc_start: 0.8479 (m-80) cc_final: 0.8074 (m-80) REVERT: B 77 MET cc_start: 0.7208 (mmt) cc_final: 0.6694 (mmt) REVERT: B 168 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6610 (mm) REVERT: B 210 ASN cc_start: 0.8714 (m110) cc_final: 0.8366 (m-40) REVERT: C 64 MET cc_start: 0.7395 (mpp) cc_final: 0.6863 (mpp) REVERT: C 129 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 198 GLU cc_start: 0.6747 (tt0) cc_final: 0.6484 (tt0) REVERT: C 287 ASN cc_start: 0.8167 (t0) cc_final: 0.7365 (m-40) REVERT: D 314 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7806 (mmmm) REVERT: F 35 SER cc_start: 0.8877 (t) cc_final: 0.8620 (p) REVERT: F 36 GLU cc_start: 0.7796 (tp30) cc_final: 0.7524 (tp30) REVERT: F 42 PHE cc_start: 0.7811 (m-80) cc_final: 0.7429 (m-10) REVERT: F 54 ASP cc_start: 0.7591 (t0) cc_final: 0.7386 (t0) REVERT: F 74 VAL cc_start: 0.7825 (t) cc_final: 0.7499 (m) REVERT: F 87 ASP cc_start: 0.8177 (t0) cc_final: 0.7860 (t0) REVERT: F 156 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7808 (ptmt) REVERT: F 214 GLN cc_start: 0.6510 (mt0) cc_final: 0.5968 (mt0) REVERT: F 254 TYR cc_start: 0.8494 (t80) cc_final: 0.8226 (t80) REVERT: F 375 ASP cc_start: 0.7323 (p0) cc_final: 0.6994 (p0) REVERT: F 388 ASN cc_start: 0.6885 (t0) cc_final: 0.6592 (t0) REVERT: F 470 LEU cc_start: 0.7874 (mt) cc_final: 0.7604 (mt) REVERT: F 510 GLU cc_start: 0.7467 (tt0) cc_final: 0.7247 (tt0) REVERT: F 522 ASP cc_start: 0.7272 (t0) cc_final: 0.7063 (t0) outliers start: 38 outliers final: 31 residues processed: 348 average time/residue: 0.1277 time to fit residues: 62.9441 Evaluate side-chains 352 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 320 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE 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 206 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 ILE 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 C residue 50 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 GLU 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 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 262 CYS 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 128 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 167 optimal weight: 0.4980 chunk 81 optimal weight: 0.1980 chunk 160 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.131050 restraints weight = 17859.785| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.90 r_work: 0.3619 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13976 Z= 0.154 Angle : 0.678 15.033 19017 Z= 0.311 Chirality : 0.043 0.196 2144 Planarity : 0.005 0.044 2430 Dihedral : 7.131 93.235 1924 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.26 % Allowed : 18.12 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.20), residues: 1728 helix: 0.42 (0.18), residues: 843 sheet: -0.21 (0.41), residues: 180 loop : -0.85 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 300 TYR 0.013 0.001 TYR F 354 PHE 0.024 0.001 PHE B 26 TRP 0.014 0.001 TRP A 293 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00369 (13967) covalent geometry : angle 0.62596 (18991) SS BOND : bond 0.00495 ( 1) SS BOND : angle 1.34779 ( 2) hydrogen bonds : bond 0.03956 ( 653) hydrogen bonds : angle 4.92957 ( 1860) metal coordination : bond 0.01037 ( 8) metal coordination : angle 7.38631 ( 24) *********************** 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 348 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 315 time to evaluate : 0.553 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: 0.6462 (mmm) cc_final: 0.6209 (mmm) REVERT: A 248 MET cc_start: 0.6843 (ppp) cc_final: 0.6641 (ppp) REVERT: A 303 TYR cc_start: 0.8537 (m-80) cc_final: 0.8153 (m-80) REVERT: B 77 MET cc_start: 0.7228 (mmt) cc_final: 0.6809 (mmt) REVERT: B 168 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6551 (mm) REVERT: B 210 ASN cc_start: 0.8722 (m110) cc_final: 0.8377 (m-40) REVERT: B 239 PHE cc_start: 0.7011 (t80) cc_final: 0.6719 (t80) REVERT: C 32 GLN cc_start: 0.7305 (pm20) cc_final: 0.7100 (pm20) REVERT: C 64 MET cc_start: 0.7375 (mpp) cc_final: 0.6862 (mpp) REVERT: C 126 THR cc_start: 0.7519 (m) cc_final: 0.7234 (p) REVERT: C 129 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 287 ASN cc_start: 0.8132 (t0) cc_final: 0.7383 (m-40) REVERT: D 314 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7799 (mmmm) REVERT: F 35 SER cc_start: 0.8863 (t) cc_final: 0.8608 (p) REVERT: F 36 GLU cc_start: 0.7762 (tp30) cc_final: 0.7499 (tp30) REVERT: F 42 PHE cc_start: 0.7830 (m-80) cc_final: 0.7442 (m-10) REVERT: F 74 VAL cc_start: 0.7846 (t) cc_final: 0.7513 (m) REVERT: F 87 ASP cc_start: 0.8205 (t0) cc_final: 0.7884 (t0) REVERT: F 254 TYR cc_start: 0.8452 (t80) cc_final: 0.8248 (t80) REVERT: F 375 ASP cc_start: 0.7283 (p0) cc_final: 0.6965 (p0) REVERT: F 388 ASN cc_start: 0.6852 (t0) cc_final: 0.6637 (t0) REVERT: F 470 LEU cc_start: 0.7864 (mt) cc_final: 0.7598 (mt) REVERT: F 522 ASP cc_start: 0.7292 (t0) cc_final: 0.7078 (t0) outliers start: 33 outliers final: 30 residues processed: 336 average time/residue: 0.1336 time to fit residues: 63.4918 Evaluate side-chains 349 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 318 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE 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 206 ILE 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 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 C residue 50 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 VAL 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 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 262 CYS 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 43 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 117 optimal weight: 0.0060 chunk 158 optimal weight: 0.4980 chunk 127 optimal weight: 0.0470 chunk 152 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 chunk 154 optimal weight: 0.7980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** F 214 GLN ** 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 = 0.3909 r_free = 0.3909 target = 0.146056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131645 restraints weight = 17633.521| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.91 r_work: 0.3629 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3540 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= 0.138 Angle : 0.662 14.034 19017 Z= 0.305 Chirality : 0.043 0.198 2144 Planarity : 0.005 0.046 2430 Dihedral : 7.034 96.462 1924 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.92 % Allowed : 18.60 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.20), residues: 1728 helix: 0.51 (0.18), residues: 844 sheet: -0.21 (0.42), residues: 182 loop : -0.83 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 300 TYR 0.012 0.001 TYR C 249 PHE 0.012 0.001 PHE B 44 TRP 0.015 0.001 TRP A 293 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00327 (13967) covalent geometry : angle 0.61630 (18991) SS BOND : bond 0.00351 ( 1) SS BOND : angle 1.40420 ( 2) hydrogen bonds : bond 0.03794 ( 653) hydrogen bonds : angle 4.90264 ( 1860) metal coordination : bond 0.00902 ( 8) metal coordination : angle 6.80601 ( 24) ********************** 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 344 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6476 (mmm) cc_final: 0.6216 (mmm) REVERT: A 185 MET cc_start: 0.7943 (tpp) cc_final: 0.7354 (tpp) REVERT: A 303 TYR cc_start: 0.8494 (m-80) cc_final: 0.7883 (m-80) REVERT: B 77 MET cc_start: 0.7233 (mmt) cc_final: 0.6489 (mmt) REVERT: B 210 ASN cc_start: 0.8729 (m110) cc_final: 0.8393 (m-40) REVERT: C 64 MET cc_start: 0.7417 (mpp) cc_final: 0.6935 (mpp) REVERT: C 69 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7682 (mt-10) REVERT: C 126 THR cc_start: 0.7428 (m) cc_final: 0.7192 (p) REVERT: C 129 GLN cc_start: 0.7394 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 287 ASN cc_start: 0.8079 (t0) cc_final: 0.7419 (m-40) REVERT: D 314 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7788 (mmmm) REVERT: F 35 SER cc_start: 0.8865 (t) cc_final: 0.8618 (p) REVERT: F 36 GLU cc_start: 0.7746 (tp30) cc_final: 0.7487 (tp30) REVERT: F 42 PHE cc_start: 0.7854 (m-80) cc_final: 0.7515 (m-10) REVERT: F 74 VAL cc_start: 0.7843 (t) cc_final: 0.7511 (m) REVERT: F 87 ASP cc_start: 0.8208 (t0) cc_final: 0.7877 (t0) REVERT: F 100 LYS cc_start: 0.7754 (mtpp) cc_final: 0.7377 (mtpp) REVERT: F 254 TYR cc_start: 0.8399 (t80) cc_final: 0.8146 (t80) REVERT: F 375 ASP cc_start: 0.7287 (p0) cc_final: 0.6966 (p0) REVERT: F 388 ASN cc_start: 0.6823 (t0) cc_final: 0.6613 (t0) REVERT: F 470 LEU cc_start: 0.7893 (mt) cc_final: 0.7628 (mt) REVERT: F 522 ASP cc_start: 0.7297 (t0) cc_final: 0.7061 (t0) outliers start: 28 outliers final: 25 residues processed: 334 average time/residue: 0.1332 time to fit residues: 62.7971 Evaluate side-chains 339 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 314 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 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 206 ILE 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 B residue 45 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 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 118 VAL Chi-restraints excluded: chain D residue 178 LEU 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 F residue 75 ILE Chi-restraints excluded: chain F residue 262 CYS 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 65 optimal weight: 0.8980 chunk 92 optimal weight: 0.0970 chunk 124 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131376 restraints weight = 17840.551| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.92 r_work: 0.3623 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 : 0.004 0.036 13976 Z= 0.148 Angle : 0.683 14.140 19017 Z= 0.315 Chirality : 0.044 0.423 2144 Planarity : 0.005 0.044 2430 Dihedral : 7.029 98.477 1924 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.33 % Allowed : 18.53 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1728 helix: 0.54 (0.18), residues: 836 sheet: -0.14 (0.42), residues: 180 loop : -0.83 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 310 TYR 0.015 0.001 TYR F 294 PHE 0.026 0.001 PHE B 26 TRP 0.014 0.001 TRP A 293 HIS 0.006 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00352 (13967) covalent geometry : angle 0.64024 (18991) SS BOND : bond 0.00466 ( 1) SS BOND : angle 1.30228 ( 2) hydrogen bonds : bond 0.03865 ( 653) hydrogen bonds : angle 4.95518 ( 1860) metal coordination : bond 0.00961 ( 8) metal coordination : angle 6.72886 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.64 seconds wall clock time: 58 minutes 48.14 seconds (3528.14 seconds total)