Starting phenix.real_space_refine on Mon Nov 18 02:56:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd9_37458/11_2024/8wd9_37458.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd9_37458/11_2024/8wd9_37458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd9_37458/11_2024/8wd9_37458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd9_37458/11_2024/8wd9_37458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd9_37458/11_2024/8wd9_37458.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd9_37458/11_2024/8wd9_37458.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3597 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 7899 2.51 5 N 2200 2.21 5 O 2230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12355 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2302 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 292} Chain: "C" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2133 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "D" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 26, 'TRANS': 490} Chain breaks: 1 Chain: "A" Number of atoms: 3964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3964 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 475} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'9XX': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.80, per 1000 atoms: 0.71 Number of scatterers: 12355 At special positions: 0 Unit cell: (92.66, 85.28, 171.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 2230 8.00 N 2200 7.00 C 7899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2958 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 10 sheets defined 49.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 1 through 9 removed outlier: 3.846A pdb=" N ALA B 6 " --> pdb=" O GLY B 2 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG B 7 " --> pdb=" O TRP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 27 removed outlier: 3.602A pdb=" N VAL B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.687A pdb=" N ALA B 36 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 38 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 40 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.591A pdb=" N GLN B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 122 Proline residue: B 96 - end of helix removed outlier: 3.800A pdb=" N ILE B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 142 removed outlier: 3.790A pdb=" N ALA B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 171 through 202 removed outlier: 5.281A pdb=" N LEU B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 4.821A pdb=" N MET B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 189 " --> pdb=" O MET B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.686A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 245 removed outlier: 4.346A pdb=" N VAL B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.819A pdb=" N THR B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 273 through 302 removed outlier: 3.919A pdb=" N SER B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 37 through 42 removed outlier: 4.445A pdb=" N PHE C 41 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 42 " --> pdb=" O PRO C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 42' Processing helix chain 'C' and resid 72 through 110 removed outlier: 3.550A pdb=" N ARG C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 144 through 173 removed outlier: 3.734A pdb=" N PHE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TRP C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Proline residue: C 158 - end of helix removed outlier: 3.668A pdb=" N ALA C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 181 through 184 removed outlier: 3.687A pdb=" N GLY C 184 " --> pdb=" O LYS C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'C' and resid 199 through 225 removed outlier: 4.428A pdb=" N VAL C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 204 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 4.066A pdb=" N GLN C 243 " --> pdb=" O ASN C 240 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR C 244 " --> pdb=" O VAL C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 244' Processing helix chain 'C' and resid 253 through 279 removed outlier: 3.567A pdb=" N ALA C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 removed outlier: 4.045A pdb=" N ALA C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 removed outlier: 4.304A pdb=" N ILE D 55 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.943A pdb=" N ASN D 103 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 104 " --> pdb=" O MET D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.701A pdb=" N GLN D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 139 removed outlier: 3.970A pdb=" N ARG D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 removed outlier: 3.539A pdb=" N GLN D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 168 removed outlier: 3.741A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.842A pdb=" N SER D 182 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA D 183 " --> pdb=" O PRO D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 179 through 183' Processing helix chain 'D' and resid 188 through 197 Processing helix chain 'D' and resid 213 through 221 removed outlier: 4.055A pdb=" N GLN D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 330 through 338 Processing helix chain 'D' and resid 362 through 368 Processing helix chain 'D' and resid 377 through 381 removed outlier: 3.951A pdb=" N SER D 380 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER D 381 " --> pdb=" O PRO D 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 377 through 381' Processing helix chain 'D' and resid 393 through 399 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.859A pdb=" N ASP D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN D 417 " --> pdb=" O GLU D 413 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 432 removed outlier: 3.773A pdb=" N LEU D 432 " --> pdb=" O PRO D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 removed outlier: 3.894A pdb=" N GLN D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.993A pdb=" N GLN D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.809A pdb=" N THR A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.790A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 removed outlier: 4.373A pdb=" N HIS A 131 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 145 removed outlier: 3.722A pdb=" N VAL A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.698A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 180' Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.969A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.895A pdb=" N LEU A 276 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.590A pdb=" N GLY A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.559A pdb=" N ILE A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.559A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 485 through 502 removed outlier: 3.750A pdb=" N SER A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.832A pdb=" N ILE A 538 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.349A pdb=" N VAL D 38 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 234 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 280 through 283 removed outlier: 3.919A pdb=" N LEU D 282 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 307 through 310 removed outlier: 5.756A pdb=" N LEU D 287 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU D 287 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER D 345 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 485 through 489 removed outlier: 3.647A pdb=" N GLY D 324 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL D 502 " --> pdb=" O HIS D 513 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS D 513 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 504 " --> pdb=" O VAL D 511 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 371 through 374 Processing sheet with id=AA6, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA7, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 85 removed outlier: 6.480A pdb=" N THR A 95 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 84 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG A 93 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.931A pdb=" N GLN A 296 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP A 511 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE A 294 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE A 513 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA A 292 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL A 515 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLY A 290 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY A 517 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR A 288 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 385 through 387 removed outlier: 6.070A pdb=" N TYR A 385 " --> pdb=" O VAL A 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 504 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2012 1.28 - 1.41: 3131 1.41 - 1.54: 7424 1.54 - 1.68: 7 1.68 - 1.81: 47 Bond restraints: 12621 Sorted by residual: bond pdb=" C PRO A 42 " pdb=" O PRO A 42 " ideal model delta sigma weight residual 1.240 1.162 0.079 1.12e-02 7.97e+03 4.92e+01 bond pdb=" C PRO C 280 " pdb=" O PRO C 280 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.30e-02 5.92e+03 4.22e+01 bond pdb=" C ILE C 262 " pdb=" O ILE C 262 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.02e-02 9.61e+03 3.94e+01 bond pdb=" C GLY A 39 " pdb=" O GLY A 39 " ideal model delta sigma weight residual 1.239 1.195 0.044 8.50e-03 1.38e+04 2.72e+01 bond pdb=" C VAL A 37 " pdb=" O VAL A 37 " ideal model delta sigma weight residual 1.239 1.178 0.061 1.22e-02 6.72e+03 2.49e+01 ... (remaining 12616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 17076 4.09 - 8.18: 129 8.18 - 12.27: 11 12.27 - 16.36: 1 16.36 - 20.45: 1 Bond angle restraints: 17218 Sorted by residual: angle pdb=" N ARG C 286 " pdb=" CA ARG C 286 " pdb=" C ARG C 286 " ideal model delta sigma weight residual 110.80 90.35 20.45 2.13e+00 2.20e-01 9.21e+01 angle pdb=" C GLU A 79 " pdb=" CA GLU A 79 " pdb=" CB GLU A 79 " ideal model delta sigma weight residual 111.65 100.44 11.21 1.44e+00 4.82e-01 6.06e+01 angle pdb=" C ALA C 284 " pdb=" CA ALA C 284 " pdb=" CB ALA C 284 " ideal model delta sigma weight residual 110.11 124.17 -14.06 1.89e+00 2.80e-01 5.53e+01 angle pdb=" N GLY A 40 " pdb=" CA GLY A 40 " pdb=" C GLY A 40 " ideal model delta sigma weight residual 111.19 101.25 9.94 1.45e+00 4.76e-01 4.70e+01 angle pdb=" N PRO A 42 " pdb=" CA PRO A 42 " pdb=" C PRO A 42 " ideal model delta sigma weight residual 110.70 102.41 8.29 1.22e+00 6.72e-01 4.62e+01 ... (remaining 17213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 7348 34.65 - 69.31: 131 69.31 - 103.96: 12 103.96 - 138.62: 3 138.62 - 173.27: 1 Dihedral angle restraints: 7495 sinusoidal: 2872 harmonic: 4623 Sorted by residual: dihedral pdb=" C LEU B 29 " pdb=" N LEU B 29 " pdb=" CA LEU B 29 " pdb=" CB LEU B 29 " ideal model delta harmonic sigma weight residual -122.60 -144.44 21.84 0 2.50e+00 1.60e-01 7.63e+01 dihedral pdb=" C ARG C 286 " pdb=" N ARG C 286 " pdb=" CA ARG C 286 " pdb=" CB ARG C 286 " ideal model delta harmonic sigma weight residual -122.60 -101.44 -21.16 0 2.50e+00 1.60e-01 7.16e+01 dihedral pdb=" N LEU B 29 " pdb=" C LEU B 29 " pdb=" CA LEU B 29 " pdb=" CB LEU B 29 " ideal model delta harmonic sigma weight residual 122.80 140.17 -17.37 0 2.50e+00 1.60e-01 4.83e+01 ... (remaining 7492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 1989 0.174 - 0.348: 12 0.348 - 0.523: 2 0.523 - 0.697: 0 0.697 - 0.871: 1 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA LEU B 29 " pdb=" N LEU B 29 " pdb=" C LEU B 29 " pdb=" CB LEU B 29 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.90e+01 chirality pdb=" CA ARG C 286 " pdb=" N ARG C 286 " pdb=" C ARG C 286 " pdb=" CB ARG C 286 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA ASP A 282 " pdb=" N ASP A 282 " pdb=" C ASP A 282 " pdb=" CB ASP A 282 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 2001 not shown) Planarity restraints: 2241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 79 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C GLU A 79 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU A 79 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL A 80 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 10 " 0.015 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" CG ASP C 10 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASP C 10 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP C 10 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 36 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C LEU A 36 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU A 36 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 2238 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 130 2.61 - 3.18: 11115 3.18 - 3.75: 17702 3.75 - 4.33: 24455 4.33 - 4.90: 42114 Nonbonded interactions: 95516 Sorted by model distance: nonbonded pdb=" OE1 GLU A 41 " pdb=" CD PRO A 42 " model vdw 2.032 3.440 nonbonded pdb=" O ILE C 73 " pdb=" OG1 THR C 77 " model vdw 2.197 3.040 nonbonded pdb=" N ARG C 286 " pdb=" O ARG C 286 " model vdw 2.201 2.496 nonbonded pdb=" NE1 TRP A 381 " pdb=" O GLY A 383 " model vdw 2.211 3.120 nonbonded pdb=" O THR A 51 " pdb=" NE2 GLN A 129 " model vdw 2.213 3.120 ... (remaining 95511 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.970 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.007 0.084 12621 Z= 0.424 Angle : 0.926 20.446 17218 Z= 0.537 Chirality : 0.058 0.871 2004 Planarity : 0.005 0.052 2241 Dihedral : 14.658 173.270 4537 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.31 % Favored : 87.44 % Rotamer: Outliers : 1.02 % Allowed : 6.53 % Favored : 92.45 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.18), residues: 1616 helix: -1.71 (0.17), residues: 721 sheet: -3.29 (0.38), residues: 146 loop : -3.78 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 12 HIS 0.005 0.001 HIS C 71 PHE 0.031 0.001 PHE C 7 TYR 0.021 0.001 TYR D 386 ARG 0.004 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.392 Fit side-chains REVERT: B 7 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7647 (ttp-110) REVERT: C 13 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7206 (mtm-85) REVERT: C 270 MET cc_start: 0.8614 (tpt) cc_final: 0.8286 (tpt) REVERT: D 471 LEU cc_start: 0.8893 (tp) cc_final: 0.8665 (mt) REVERT: A 239 LYS cc_start: 0.8720 (mppt) cc_final: 0.8467 (mmmt) outliers start: 13 outliers final: 7 residues processed: 141 average time/residue: 0.3027 time to fit residues: 58.5315 Evaluate side-chains 99 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 259 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.0030 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN C 138 GLN C 198 ASN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 252 ASN A 264 ASN A 408 ASN A 464 ASN A 490 HIS A 497 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12621 Z= 0.200 Angle : 0.666 7.768 17218 Z= 0.338 Chirality : 0.045 0.192 2004 Planarity : 0.005 0.044 2241 Dihedral : 9.284 154.709 1850 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.89 % Allowed : 10.78 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.20), residues: 1616 helix: -0.60 (0.19), residues: 731 sheet: -2.81 (0.41), residues: 141 loop : -3.32 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 112 HIS 0.006 0.001 HIS A 306 PHE 0.016 0.001 PHE D 350 TYR 0.009 0.001 TYR B 206 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.343 Fit side-chains REVERT: B 7 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7453 (ttp-110) REVERT: B 77 ASP cc_start: 0.8615 (t0) cc_final: 0.8409 (t0) REVERT: C 270 MET cc_start: 0.8599 (tpt) cc_final: 0.8378 (tpt) REVERT: D 385 MET cc_start: 0.8560 (mtt) cc_final: 0.8210 (mtt) REVERT: A 239 LYS cc_start: 0.8739 (mppt) cc_final: 0.8454 (mmmt) REVERT: A 259 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8841 (m-30) REVERT: A 504 MET cc_start: 0.7762 (tpp) cc_final: 0.7426 (tpp) outliers start: 24 outliers final: 12 residues processed: 117 average time/residue: 0.2782 time to fit residues: 46.5440 Evaluate side-chains 102 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.0040 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.0050 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN B 201 ASN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN A 252 ASN A 431 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12621 Z= 0.184 Angle : 0.645 13.642 17218 Z= 0.320 Chirality : 0.044 0.196 2004 Planarity : 0.004 0.046 2241 Dihedral : 7.878 116.806 1839 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.44 % Allowed : 12.82 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.21), residues: 1616 helix: -0.17 (0.20), residues: 736 sheet: -2.62 (0.41), residues: 151 loop : -3.10 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 112 HIS 0.004 0.001 HIS A 306 PHE 0.013 0.001 PHE D 350 TYR 0.009 0.001 TYR B 206 ARG 0.003 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.368 Fit side-chains REVERT: B 77 ASP cc_start: 0.8595 (t0) cc_final: 0.8341 (t0) REVERT: C 270 MET cc_start: 0.8612 (tpt) cc_final: 0.8344 (tpt) REVERT: A 239 LYS cc_start: 0.8699 (mppt) cc_final: 0.8321 (mmtm) REVERT: A 259 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8816 (m-30) REVERT: A 504 MET cc_start: 0.7676 (tpp) cc_final: 0.7366 (tpp) outliers start: 31 outliers final: 15 residues processed: 128 average time/residue: 0.2574 time to fit residues: 47.7647 Evaluate side-chains 108 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 75 optimal weight: 0.0570 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN B 201 ASN D 121 ASN ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS A 431 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12621 Z= 0.152 Angle : 0.607 10.700 17218 Z= 0.301 Chirality : 0.043 0.210 2004 Planarity : 0.004 0.047 2241 Dihedral : 7.242 96.067 1835 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.52 % Allowed : 14.00 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.21), residues: 1616 helix: 0.19 (0.20), residues: 737 sheet: -2.35 (0.41), residues: 150 loop : -2.70 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 112 HIS 0.003 0.001 HIS D 399 PHE 0.014 0.001 PHE A 425 TYR 0.010 0.001 TYR D 150 ARG 0.004 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.492 Fit side-chains REVERT: B 77 ASP cc_start: 0.8596 (t0) cc_final: 0.8339 (t0) REVERT: C 55 MET cc_start: 0.8166 (mmm) cc_final: 0.7903 (mmm) REVERT: C 270 MET cc_start: 0.8578 (tpt) cc_final: 0.8343 (tpt) REVERT: D 470 ILE cc_start: 0.8646 (pt) cc_final: 0.8279 (mt) REVERT: D 480 ASP cc_start: 0.7197 (m-30) cc_final: 0.6864 (m-30) REVERT: D 495 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8758 (tt) REVERT: A 239 LYS cc_start: 0.8674 (mppt) cc_final: 0.8303 (mmtm) REVERT: A 504 MET cc_start: 0.7547 (tpp) cc_final: 0.7282 (tpp) outliers start: 32 outliers final: 14 residues processed: 134 average time/residue: 0.2238 time to fit residues: 44.9928 Evaluate side-chains 107 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 HIS B 201 ASN A 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12621 Z= 0.210 Angle : 0.628 9.928 17218 Z= 0.310 Chirality : 0.044 0.189 2004 Planarity : 0.004 0.047 2241 Dihedral : 7.068 99.156 1831 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.52 % Allowed : 15.03 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1616 helix: 0.24 (0.20), residues: 744 sheet: -2.42 (0.40), residues: 159 loop : -2.57 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 112 HIS 0.003 0.001 HIS C 71 PHE 0.014 0.001 PHE D 367 TYR 0.008 0.001 TYR C 176 ARG 0.004 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.343 Fit side-chains REVERT: B 77 ASP cc_start: 0.8642 (t0) cc_final: 0.8392 (t0) REVERT: B 185 MET cc_start: 0.8793 (tpp) cc_final: 0.8492 (ttt) REVERT: C 270 MET cc_start: 0.8579 (tpt) cc_final: 0.8308 (tpt) REVERT: D 470 ILE cc_start: 0.8674 (pt) cc_final: 0.8282 (mt) REVERT: D 495 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8759 (tt) REVERT: A 239 LYS cc_start: 0.8705 (mppt) cc_final: 0.8305 (mmtm) REVERT: A 504 MET cc_start: 0.7498 (tpp) cc_final: 0.7243 (tpp) outliers start: 32 outliers final: 20 residues processed: 121 average time/residue: 0.2381 time to fit residues: 42.5720 Evaluate side-chains 109 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.0020 chunk 139 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.0270 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN B 201 ASN ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12621 Z= 0.141 Angle : 0.612 13.129 17218 Z= 0.298 Chirality : 0.043 0.227 2004 Planarity : 0.004 0.047 2241 Dihedral : 6.913 99.434 1831 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.20 % Allowed : 15.74 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1616 helix: 0.45 (0.20), residues: 734 sheet: -2.06 (0.42), residues: 150 loop : -2.47 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 112 HIS 0.027 0.001 HIS A 306 PHE 0.015 0.001 PHE A 425 TYR 0.008 0.001 TYR B 206 ARG 0.003 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.417 Fit side-chains REVERT: B 77 ASP cc_start: 0.8601 (t0) cc_final: 0.8360 (t0) REVERT: B 185 MET cc_start: 0.8711 (tpp) cc_final: 0.8451 (ttt) REVERT: C 55 MET cc_start: 0.8081 (mmm) cc_final: 0.7869 (mmm) REVERT: C 270 MET cc_start: 0.8567 (tpt) cc_final: 0.8338 (tpt) REVERT: D 470 ILE cc_start: 0.8580 (pt) cc_final: 0.8256 (mt) REVERT: D 480 ASP cc_start: 0.7242 (m-30) cc_final: 0.7035 (m-30) REVERT: D 495 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8734 (tt) REVERT: A 239 LYS cc_start: 0.8706 (mppt) cc_final: 0.8268 (mmtm) REVERT: A 504 MET cc_start: 0.7415 (tpp) cc_final: 0.7206 (tpp) outliers start: 28 outliers final: 19 residues processed: 125 average time/residue: 0.2459 time to fit residues: 45.8292 Evaluate side-chains 107 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0050 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12621 Z= 0.151 Angle : 0.607 10.576 17218 Z= 0.295 Chirality : 0.043 0.190 2004 Planarity : 0.004 0.046 2241 Dihedral : 6.446 82.809 1831 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.44 % Allowed : 16.60 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1616 helix: 0.54 (0.20), residues: 740 sheet: -1.87 (0.42), residues: 150 loop : -2.32 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 112 HIS 0.004 0.001 HIS D 247 PHE 0.020 0.001 PHE D 350 TYR 0.007 0.001 TYR B 206 ARG 0.002 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.417 Fit side-chains REVERT: B 77 ASP cc_start: 0.8603 (t0) cc_final: 0.8384 (t0) REVERT: C 270 MET cc_start: 0.8543 (tpt) cc_final: 0.8341 (tpt) REVERT: D 470 ILE cc_start: 0.8558 (pt) cc_final: 0.8270 (mt) REVERT: D 495 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8718 (tt) REVERT: A 239 LYS cc_start: 0.8695 (mppt) cc_final: 0.8272 (mmtm) outliers start: 31 outliers final: 21 residues processed: 122 average time/residue: 0.2418 time to fit residues: 43.7897 Evaluate side-chains 113 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN D 399 HIS A 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12621 Z= 0.269 Angle : 0.658 11.821 17218 Z= 0.321 Chirality : 0.045 0.180 2004 Planarity : 0.004 0.047 2241 Dihedral : 6.462 73.522 1831 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.20 % Allowed : 17.15 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.22), residues: 1616 helix: 0.48 (0.20), residues: 744 sheet: -1.86 (0.43), residues: 140 loop : -2.38 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 112 HIS 0.030 0.001 HIS A 306 PHE 0.020 0.001 PHE D 350 TYR 0.010 0.001 TYR C 176 ARG 0.002 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 1.463 Fit side-chains REVERT: B 77 ASP cc_start: 0.8630 (t0) cc_final: 0.8398 (t0) REVERT: C 270 MET cc_start: 0.8580 (tpt) cc_final: 0.8295 (tpt) REVERT: D 495 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8776 (tt) REVERT: A 239 LYS cc_start: 0.8702 (mppt) cc_final: 0.8291 (mmtm) outliers start: 28 outliers final: 23 residues processed: 111 average time/residue: 0.2503 time to fit residues: 40.9842 Evaluate side-chains 109 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN A 127 GLN A 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12621 Z= 0.258 Angle : 0.654 10.384 17218 Z= 0.321 Chirality : 0.046 0.193 2004 Planarity : 0.004 0.047 2241 Dihedral : 6.460 70.576 1831 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.20 % Allowed : 17.31 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1616 helix: 0.41 (0.20), residues: 755 sheet: -1.84 (0.44), residues: 140 loop : -2.37 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 112 HIS 0.006 0.001 HIS A 306 PHE 0.020 0.001 PHE D 350 TYR 0.010 0.001 TYR C 176 ARG 0.003 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.296 Fit side-chains REVERT: B 77 ASP cc_start: 0.8641 (t0) cc_final: 0.8426 (t0) REVERT: C 270 MET cc_start: 0.8570 (tpt) cc_final: 0.8290 (tpt) REVERT: D 495 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8775 (tt) REVERT: A 239 LYS cc_start: 0.8771 (mppt) cc_final: 0.8290 (mmtm) outliers start: 28 outliers final: 26 residues processed: 114 average time/residue: 0.2369 time to fit residues: 40.2827 Evaluate side-chains 114 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 0.0370 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 0.0470 chunk 77 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN A 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12621 Z= 0.152 Angle : 0.640 17.184 17218 Z= 0.307 Chirality : 0.044 0.187 2004 Planarity : 0.004 0.047 2241 Dihedral : 6.293 69.515 1831 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.12 % Allowed : 17.62 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1616 helix: 0.60 (0.20), residues: 744 sheet: -1.69 (0.45), residues: 140 loop : -2.20 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 112 HIS 0.007 0.001 HIS A 306 PHE 0.024 0.001 PHE A 422 TYR 0.008 0.001 TYR B 206 ARG 0.003 0.000 ARG D 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 1.371 Fit side-chains REVERT: C 270 MET cc_start: 0.8546 (tpt) cc_final: 0.8325 (tpt) REVERT: D 495 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8730 (tt) REVERT: A 239 LYS cc_start: 0.8726 (mppt) cc_final: 0.8281 (mmtm) outliers start: 27 outliers final: 23 residues processed: 115 average time/residue: 0.2290 time to fit residues: 39.9584 Evaluate side-chains 112 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 117 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 111 optimal weight: 0.0270 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN A 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.085152 restraints weight = 22007.233| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.22 r_work: 0.2919 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12621 Z= 0.147 Angle : 0.627 15.973 17218 Z= 0.301 Chirality : 0.044 0.224 2004 Planarity : 0.004 0.046 2241 Dihedral : 6.117 68.424 1831 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.05 % Allowed : 18.02 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1616 helix: 0.70 (0.20), residues: 741 sheet: -1.56 (0.45), residues: 140 loop : -2.14 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 112 HIS 0.004 0.001 HIS D 247 PHE 0.019 0.001 PHE D 350 TYR 0.008 0.001 TYR B 206 ARG 0.003 0.000 ARG D 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2639.10 seconds wall clock time: 48 minutes 34.62 seconds (2914.62 seconds total)