Starting phenix.real_space_refine on Sat Aug 23 23:00:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wda_37459/08_2025/8wda_37459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wda_37459/08_2025/8wda_37459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wda_37459/08_2025/8wda_37459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wda_37459/08_2025/8wda_37459.map" model { file = "/net/cci-nas-00/data/ceres_data/8wda_37459/08_2025/8wda_37459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wda_37459/08_2025/8wda_37459.cif" } 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= -0.001 sd= 0.056 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 3598 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 7897 2.51 5 N 2205 2.21 5 O 2231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12359 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3962 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 475} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2233 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2123 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 23 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3975 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 27, 'TRANS': 496} Chain breaks: 1 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: 2.58, per 1000 atoms: 0.21 Number of scatterers: 12359 At special positions: 0 Unit cell: (86.92, 94.3, 164.82, 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 2231 8.00 N 2205 7.00 C 7897 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: 0.70 Conformation dependent library (CDL) restraints added in 376.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 11 sheets defined 48.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.704A pdb=" N THR A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 4.865A pdb=" N ILE A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.787A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 178 through 182 removed outlier: 4.203A pdb=" N GLY A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.608A pdb=" N PHE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 200' Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.809A pdb=" N LEU A 276 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 319 through 322 removed outlier: 3.598A pdb=" N ALA A 322 " --> pdb=" O LEU A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 322' Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.592A pdb=" N GLN A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.731A pdb=" N ARG A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 421 through 431 removed outlier: 6.240A pdb=" N THR A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 490 through 504 removed outlier: 3.719A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.166A pdb=" N ALA B 6 " --> pdb=" O GLY B 2 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 7 " --> pdb=" O TRP B 3 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) Proline residue: B 14 - end of helix removed outlier: 3.967A pdb=" N LEU B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.709A pdb=" N ARG B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.533A pdb=" N GLN B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 Proline residue: B 96 - end of helix removed outlier: 3.813A pdb=" N ILE B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.949A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 removed outlier: 3.581A pdb=" N ILE B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.694A pdb=" N GLY B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 202 removed outlier: 3.599A pdb=" N ALA B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.886A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.664A pdb=" N GLY B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 273 through 302 removed outlier: 3.756A pdb=" N VAL B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.605A pdb=" N ARG B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 307' Processing helix chain 'C' and resid 7 through 16 removed outlier: 3.863A pdb=" N ALA C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.673A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 72 through 106 removed outlier: 3.591A pdb=" N ARG C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.549A pdb=" N ALA C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.693A pdb=" N PHE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.533A pdb=" N GLU C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 224 removed outlier: 4.031A pdb=" N VAL C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 253 through 279 removed outlier: 3.595A pdb=" N ALA C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.770A pdb=" N THR D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.629A pdb=" N ARG D 86 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 116 Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.682A pdb=" N LEU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.739A pdb=" N ARG D 149 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.714A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 removed outlier: 3.834A pdb=" N GLN D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.729A pdb=" N THR D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 removed outlier: 3.609A pdb=" N ARG D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 393 removed outlier: 3.566A pdb=" N ILE D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 399 removed outlier: 3.966A pdb=" N HIS D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 removed outlier: 3.530A pdb=" N ARG D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.508A pdb=" N GLU D 431 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 432 " --> pdb=" O PRO D 429 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER D 433 " --> pdb=" O ARG D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 428 through 433' Processing helix chain 'D' and resid 437 through 446 removed outlier: 3.668A pdb=" N ALA D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 475 removed outlier: 3.648A pdb=" N ALA D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.884A pdb=" N ALA D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 475 through 480' Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.858A pdb=" N ALA D 534 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 535 " --> pdb=" O LEU D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 531 through 535' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 86 removed outlier: 4.025A pdb=" N SER A 83 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.808A pdb=" N GLN A 296 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP A 511 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 294 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 513 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA A 292 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 515 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY A 290 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY A 517 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR A 288 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 442 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN A 390 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N GLY A 441 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 385 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA A 417 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 387 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLN A 419 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 389 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 12 through 18 removed outlier: 7.080A pdb=" N GLY D 13 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 68 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU D 15 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 17 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.854A pdb=" N GLU D 234 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG D 228 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.732A pdb=" N ARG D 75 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 282 through 293 removed outlier: 7.098A pdb=" N VAL D 283 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG D 313 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER D 285 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER D 311 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 287 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 307 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR D 291 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG D 305 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU D 293 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU D 303 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 372 through 374 removed outlier: 7.390A pdb=" N GLN D 372 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP D 456 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL D 374 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 453 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE D 488 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 455 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA D 321 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET D 505 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 323 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL D 502 " --> pdb=" O HIS D 513 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS D 513 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL D 504 " --> pdb=" O VAL D 511 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1353 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: 1.42 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2013 1.31 - 1.43: 3302 1.43 - 1.56: 7258 1.56 - 1.68: 0 1.68 - 1.81: 47 Bond restraints: 12620 Sorted by residual: bond pdb=" CA ALA D 257 " pdb=" C ALA D 257 " ideal model delta sigma weight residual 1.527 1.474 0.053 1.31e-02 5.83e+03 1.63e+01 bond pdb=" O 9XX A 602 " pdb=" C15 9XX A 602 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C18 9XX A 602 " pdb=" O1 9XX A 602 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N ALA D 257 " pdb=" CA ALA D 257 " ideal model delta sigma weight residual 1.458 1.416 0.042 1.48e-02 4.57e+03 8.02e+00 bond pdb=" CA PRO D 258 " pdb=" CB PRO D 258 " ideal model delta sigma weight residual 1.534 1.499 0.035 1.40e-02 5.10e+03 6.10e+00 ... (remaining 12615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 16932 2.41 - 4.83: 236 4.83 - 7.24: 38 7.24 - 9.65: 3 9.65 - 12.07: 1 Bond angle restraints: 17210 Sorted by residual: angle pdb=" N VAL A 90 " pdb=" CA VAL A 90 " pdb=" C VAL A 90 " ideal model delta sigma weight residual 113.71 108.42 5.29 9.50e-01 1.11e+00 3.10e+01 angle pdb=" N ALA D 257 " pdb=" CA ALA D 257 " pdb=" C ALA D 257 " ideal model delta sigma weight residual 110.07 104.31 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" N ARG B 7 " pdb=" CA ARG B 7 " pdb=" C ARG B 7 " ideal model delta sigma weight residual 113.41 108.35 5.06 1.22e+00 6.72e-01 1.72e+01 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 111.90 108.80 3.10 8.10e-01 1.52e+00 1.47e+01 angle pdb=" N LEU B 215 " pdb=" CA LEU B 215 " pdb=" C LEU B 215 " ideal model delta sigma weight residual 110.35 115.67 -5.32 1.40e+00 5.10e-01 1.45e+01 ... (remaining 17205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 7355 34.47 - 68.93: 127 68.93 - 103.40: 12 103.40 - 137.87: 3 137.87 - 172.33: 1 Dihedral angle restraints: 7498 sinusoidal: 2875 harmonic: 4623 Sorted by residual: dihedral pdb=" C THR D 261 " pdb=" N THR D 261 " pdb=" CA THR D 261 " pdb=" CB THR D 261 " ideal model delta harmonic sigma weight residual -122.00 -137.85 15.85 0 2.50e+00 1.60e-01 4.02e+01 dihedral pdb=" N THR D 261 " pdb=" C THR D 261 " pdb=" CA THR D 261 " pdb=" CB THR D 261 " ideal model delta harmonic sigma weight residual 123.40 137.67 -14.27 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" C16 9XX A 602 " pdb=" O 9XX A 602 " pdb=" C15 9XX A 602 " pdb=" O6 9XX A 602 " ideal model delta sinusoidal sigma weight residual -2.46 169.87 -172.33 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1978 0.124 - 0.247: 24 0.247 - 0.371: 1 0.371 - 0.495: 0 0.495 - 0.618: 1 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA THR D 261 " pdb=" N THR D 261 " pdb=" C THR D 261 " pdb=" CB THR D 261 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" CA ARG B 7 " pdb=" N ARG B 7 " pdb=" C ARG B 7 " pdb=" CB ARG B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA SER D 259 " pdb=" N SER D 259 " pdb=" C SER D 259 " pdb=" CB SER D 259 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 2001 not shown) Planarity restraints: 2239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 192 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C LEU C 192 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU C 192 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG C 193 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 257 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO D 258 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 60 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO B 61 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " -0.036 5.00e-02 4.00e+02 ... (remaining 2236 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2236 2.76 - 3.30: 11537 3.30 - 3.83: 18849 3.83 - 4.37: 22967 4.37 - 4.90: 40319 Nonbonded interactions: 95908 Sorted by model distance: nonbonded pdb=" OH TYR A 70 " pdb=" O LEU A 178 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" OD2 ASP A 503 " model vdw 2.243 3.040 nonbonded pdb=" NE2 GLN D 160 " pdb=" O PRO D 180 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP A 259 " pdb=" OG1 THR B 165 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP C 45 " pdb=" OG1 THR C 47 " model vdw 2.313 3.040 ... (remaining 95903 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 : 0.005 0.292 12622 Z= 0.335 Angle : 0.724 12.065 17210 Z= 0.410 Chirality : 0.048 0.618 2004 Planarity : 0.005 0.070 2239 Dihedral : 14.237 172.335 4538 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 0.55 % Allowed : 4.49 % Favored : 94.96 % Cbeta Deviations : 0.07 % 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: -4.40 (0.18), residues: 1612 helix: -2.61 (0.16), residues: 742 sheet: -2.40 (0.40), residues: 153 loop : -3.34 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 33 TYR 0.022 0.001 TYR D 354 PHE 0.013 0.001 PHE A 165 TRP 0.018 0.001 TRP C 12 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00412 (12620) covalent geometry : angle 0.72450 (17210) hydrogen bonds : bond 0.14129 ( 464) hydrogen bonds : angle 6.45991 ( 1353) Misc. bond : bond 0.21265 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.439 Fit side-chains REVERT: B 28 PHE cc_start: 0.7962 (t80) cc_final: 0.7579 (t80) REVERT: B 68 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7225 (ttm-80) REVERT: C 112 TRP cc_start: 0.7411 (t60) cc_final: 0.6876 (t-100) REVERT: D 404 ARG cc_start: 0.7321 (mmt180) cc_final: 0.7024 (mtm-85) outliers start: 7 outliers final: 2 residues processed: 132 average time/residue: 0.1210 time to fit residues: 21.4946 Evaluate side-chains 94 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain C residue 286 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 497 GLN B 65 GLN B 152 GLN B 201 ASN B 224 HIS C 138 GLN C 198 ASN D 103 ASN D 363 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.079372 restraints weight = 20954.908| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.30 r_work: 0.2771 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12622 Z= 0.157 Angle : 0.623 11.899 17210 Z= 0.319 Chirality : 0.045 0.166 2004 Planarity : 0.005 0.067 2239 Dihedral : 8.688 140.014 1835 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.18 % Allowed : 9.13 % Favored : 89.69 % 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: -3.20 (0.20), residues: 1612 helix: -1.54 (0.19), residues: 720 sheet: -1.86 (0.41), residues: 156 loop : -2.77 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 84 TYR 0.019 0.001 TYR D 354 PHE 0.012 0.001 PHE A 165 TRP 0.012 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00369 (12620) covalent geometry : angle 0.62308 (17210) hydrogen bonds : bond 0.04383 ( 464) hydrogen bonds : angle 4.90941 ( 1353) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.484 Fit side-chains REVERT: B 28 PHE cc_start: 0.7809 (t80) cc_final: 0.7520 (t80) REVERT: B 68 ARG cc_start: 0.7658 (mmt180) cc_final: 0.7106 (ttm-80) REVERT: B 215 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8220 (pp) REVERT: C 7 PHE cc_start: 0.5280 (t80) cc_final: 0.4717 (t80) REVERT: C 112 TRP cc_start: 0.8038 (t60) cc_final: 0.7090 (t-100) REVERT: C 175 ASP cc_start: 0.8996 (p0) cc_final: 0.8638 (p0) REVERT: C 276 ASP cc_start: 0.8243 (m-30) cc_final: 0.7956 (m-30) REVERT: C 283 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7249 (ttm170) REVERT: D 404 ARG cc_start: 0.7481 (mmt180) cc_final: 0.6933 (mtm-85) REVERT: D 430 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8689 (mtp-110) outliers start: 15 outliers final: 4 residues processed: 120 average time/residue: 0.1457 time to fit residues: 23.9675 Evaluate side-chains 100 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 152 GLN B 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.079149 restraints weight = 21251.845| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.37 r_work: 0.2768 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12622 Z= 0.154 Angle : 0.605 11.824 17210 Z= 0.308 Chirality : 0.044 0.152 2004 Planarity : 0.004 0.066 2239 Dihedral : 8.212 120.621 1830 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.97 % Allowed : 9.84 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.20), residues: 1612 helix: -1.11 (0.19), residues: 723 sheet: -1.60 (0.42), residues: 158 loop : -2.43 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 361 TYR 0.018 0.001 TYR D 354 PHE 0.012 0.001 PHE A 165 TRP 0.011 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00364 (12620) covalent geometry : angle 0.60492 (17210) hydrogen bonds : bond 0.04227 ( 464) hydrogen bonds : angle 4.73354 ( 1353) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 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: 25 poor density : 103 time to evaluate : 0.494 Fit side-chains REVERT: A 85 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 28 PHE cc_start: 0.7683 (t80) cc_final: 0.7417 (t80) REVERT: B 68 ARG cc_start: 0.7652 (mmt180) cc_final: 0.7091 (ttm-80) REVERT: B 176 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8891 (tt) REVERT: B 215 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8213 (pp) REVERT: C 13 ARG cc_start: 0.7875 (mpt180) cc_final: 0.7664 (mpt-90) REVERT: C 112 TRP cc_start: 0.8014 (t60) cc_final: 0.7095 (t-100) REVERT: C 175 ASP cc_start: 0.8924 (p0) cc_final: 0.8581 (p0) REVERT: C 276 ASP cc_start: 0.8262 (m-30) cc_final: 0.8041 (m-30) REVERT: C 283 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7148 (ttm170) REVERT: D 404 ARG cc_start: 0.7462 (mmt180) cc_final: 0.6932 (mtm-85) outliers start: 25 outliers final: 10 residues processed: 123 average time/residue: 0.1377 time to fit residues: 23.9004 Evaluate side-chains 104 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 152 GLN B 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.078255 restraints weight = 21260.947| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.35 r_work: 0.2746 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12622 Z= 0.197 Angle : 0.630 12.754 17210 Z= 0.320 Chirality : 0.045 0.153 2004 Planarity : 0.005 0.064 2239 Dihedral : 8.079 115.763 1830 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.89 % Allowed : 11.73 % Favored : 86.38 % 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: -2.37 (0.21), residues: 1612 helix: -0.90 (0.19), residues: 722 sheet: -1.31 (0.44), residues: 151 loop : -2.30 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 361 TYR 0.021 0.001 TYR D 354 PHE 0.014 0.001 PHE A 165 TRP 0.012 0.001 TRP A 518 HIS 0.005 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00470 (12620) covalent geometry : angle 0.63000 (17210) hydrogen bonds : bond 0.04577 ( 464) hydrogen bonds : angle 4.75841 ( 1353) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 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: 24 poor density : 102 time to evaluate : 0.431 Fit side-chains REVERT: A 85 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8106 (tm-30) REVERT: B 28 PHE cc_start: 0.7729 (t80) cc_final: 0.7519 (t80) REVERT: B 68 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7141 (ttm-80) REVERT: B 95 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8257 (t80) REVERT: B 185 MET cc_start: 0.8501 (tpt) cc_final: 0.7795 (mmm) REVERT: B 215 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8334 (pp) REVERT: C 112 TRP cc_start: 0.8030 (t60) cc_final: 0.7080 (t-100) REVERT: C 175 ASP cc_start: 0.8932 (p0) cc_final: 0.8604 (p0) REVERT: C 276 ASP cc_start: 0.8313 (m-30) cc_final: 0.8067 (m-30) REVERT: C 283 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7072 (ttm170) REVERT: D 404 ARG cc_start: 0.7510 (mmt180) cc_final: 0.6996 (mtm-85) outliers start: 24 outliers final: 12 residues processed: 120 average time/residue: 0.1365 time to fit residues: 23.0245 Evaluate side-chains 107 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 130 optimal weight: 0.0010 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.080671 restraints weight = 21032.334| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.34 r_work: 0.2794 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12622 Z= 0.112 Angle : 0.572 11.093 17210 Z= 0.291 Chirality : 0.043 0.160 2004 Planarity : 0.004 0.065 2239 Dihedral : 7.741 113.798 1830 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.81 % Allowed : 12.76 % Favored : 85.43 % 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: -2.02 (0.21), residues: 1612 helix: -0.63 (0.20), residues: 728 sheet: -1.15 (0.46), residues: 147 loop : -2.09 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 286 TYR 0.013 0.001 TYR D 354 PHE 0.009 0.001 PHE A 165 TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00254 (12620) covalent geometry : angle 0.57202 (17210) hydrogen bonds : bond 0.03692 ( 464) hydrogen bonds : angle 4.55997 ( 1353) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.346 Fit side-chains REVERT: A 85 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 104 ASP cc_start: 0.8395 (t0) cc_final: 0.8186 (t0) REVERT: B 28 PHE cc_start: 0.7530 (t80) cc_final: 0.7300 (t80) REVERT: B 68 ARG cc_start: 0.7641 (mmt180) cc_final: 0.7263 (ttm-80) REVERT: B 95 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8257 (t80) REVERT: B 185 MET cc_start: 0.8498 (tpt) cc_final: 0.7779 (mmm) REVERT: B 215 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8207 (pp) REVERT: C 112 TRP cc_start: 0.7952 (t60) cc_final: 0.7089 (t-100) REVERT: C 175 ASP cc_start: 0.8898 (p0) cc_final: 0.8586 (p0) REVERT: C 276 ASP cc_start: 0.8267 (m-30) cc_final: 0.7849 (m-30) REVERT: C 283 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7349 (ttm170) REVERT: D 404 ARG cc_start: 0.7433 (mmt180) cc_final: 0.6989 (mtm-85) outliers start: 23 outliers final: 12 residues processed: 125 average time/residue: 0.1256 time to fit residues: 22.3121 Evaluate side-chains 110 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 0.3980 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN B 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.081371 restraints weight = 20973.755| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.33 r_work: 0.2806 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12622 Z= 0.108 Angle : 0.560 10.413 17210 Z= 0.285 Chirality : 0.043 0.185 2004 Planarity : 0.004 0.064 2239 Dihedral : 7.488 112.128 1830 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.89 % Allowed : 12.99 % Favored : 85.12 % 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: -1.74 (0.21), residues: 1612 helix: -0.39 (0.20), residues: 728 sheet: -1.01 (0.47), residues: 147 loop : -1.95 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 286 TYR 0.011 0.001 TYR D 354 PHE 0.008 0.001 PHE A 165 TRP 0.009 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00245 (12620) covalent geometry : angle 0.55968 (17210) hydrogen bonds : bond 0.03499 ( 464) hydrogen bonds : angle 4.43626 ( 1353) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.523 Fit side-chains REVERT: A 85 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7656 (mp0) REVERT: A 104 ASP cc_start: 0.8381 (t0) cc_final: 0.8165 (t0) REVERT: B 28 PHE cc_start: 0.7533 (t80) cc_final: 0.7294 (t80) REVERT: B 68 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7278 (ttm-80) REVERT: B 95 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8266 (t80) REVERT: B 185 MET cc_start: 0.8490 (tpt) cc_final: 0.7903 (mpp) REVERT: B 215 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8212 (pp) REVERT: C 112 TRP cc_start: 0.7933 (t60) cc_final: 0.7103 (t-100) REVERT: C 175 ASP cc_start: 0.8857 (p0) cc_final: 0.8584 (p0) REVERT: C 276 ASP cc_start: 0.8282 (m-30) cc_final: 0.8046 (m-30) REVERT: D 404 ARG cc_start: 0.7380 (mmt180) cc_final: 0.6892 (mtm-85) outliers start: 24 outliers final: 17 residues processed: 122 average time/residue: 0.1320 time to fit residues: 22.8498 Evaluate side-chains 115 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 13 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 159 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.081276 restraints weight = 20921.934| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.36 r_work: 0.2803 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12622 Z= 0.114 Angle : 0.570 12.264 17210 Z= 0.287 Chirality : 0.043 0.151 2004 Planarity : 0.004 0.064 2239 Dihedral : 7.331 110.838 1830 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.81 % Allowed : 13.31 % Favored : 84.88 % 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: -1.51 (0.21), residues: 1612 helix: -0.11 (0.20), residues: 721 sheet: -0.85 (0.47), residues: 145 loop : -1.93 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 286 TYR 0.013 0.001 TYR D 354 PHE 0.009 0.001 PHE A 165 TRP 0.009 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00264 (12620) covalent geometry : angle 0.56973 (17210) hydrogen bonds : bond 0.03512 ( 464) hydrogen bonds : angle 4.37813 ( 1353) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.523 Fit side-chains REVERT: A 85 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7571 (mp0) REVERT: A 104 ASP cc_start: 0.8411 (t0) cc_final: 0.8186 (t0) REVERT: B 28 PHE cc_start: 0.7441 (t80) cc_final: 0.7209 (t80) REVERT: B 68 ARG cc_start: 0.7611 (mmt180) cc_final: 0.7221 (ttm-80) REVERT: B 95 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8234 (t80) REVERT: B 185 MET cc_start: 0.8487 (tpt) cc_final: 0.7759 (mmm) REVERT: B 215 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8162 (pp) REVERT: C 112 TRP cc_start: 0.7923 (t60) cc_final: 0.7095 (t-100) REVERT: C 175 ASP cc_start: 0.8846 (p0) cc_final: 0.8582 (p0) REVERT: C 276 ASP cc_start: 0.8380 (m-30) cc_final: 0.8003 (m-30) REVERT: D 404 ARG cc_start: 0.7312 (mmt180) cc_final: 0.6823 (mtm-85) outliers start: 23 outliers final: 18 residues processed: 121 average time/residue: 0.1486 time to fit residues: 25.0435 Evaluate side-chains 120 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 145 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 126 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.079232 restraints weight = 21009.114| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.34 r_work: 0.2766 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12622 Z= 0.175 Angle : 0.614 11.869 17210 Z= 0.310 Chirality : 0.045 0.211 2004 Planarity : 0.004 0.062 2239 Dihedral : 7.414 109.292 1830 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.13 % Allowed : 13.86 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.59 (0.21), residues: 1612 helix: -0.16 (0.20), residues: 726 sheet: -0.86 (0.46), residues: 149 loop : -2.01 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 129 TYR 0.021 0.001 TYR D 354 PHE 0.013 0.001 PHE A 165 TRP 0.011 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00417 (12620) covalent geometry : angle 0.61409 (17210) hydrogen bonds : bond 0.04198 ( 464) hydrogen bonds : angle 4.52852 ( 1353) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.511 Fit side-chains REVERT: A 85 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7631 (mp0) REVERT: B 28 PHE cc_start: 0.7529 (t80) cc_final: 0.7305 (t80) REVERT: B 68 ARG cc_start: 0.7652 (mmt180) cc_final: 0.7299 (ttm-80) REVERT: B 95 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8283 (t80) REVERT: B 185 MET cc_start: 0.8550 (tpt) cc_final: 0.7935 (mpp) REVERT: B 215 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8260 (pp) REVERT: C 112 TRP cc_start: 0.7952 (t60) cc_final: 0.7097 (t-100) REVERT: C 175 ASP cc_start: 0.8871 (p0) cc_final: 0.8566 (p0) REVERT: C 276 ASP cc_start: 0.8425 (m-30) cc_final: 0.8057 (m-30) REVERT: D 404 ARG cc_start: 0.7297 (mmt180) cc_final: 0.6825 (mtm-85) REVERT: D 406 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8090 (mt0) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.1428 time to fit residues: 23.5240 Evaluate side-chains 114 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 406 GLN Chi-restraints excluded: chain D residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.081390 restraints weight = 20917.074| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.36 r_work: 0.2802 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12622 Z= 0.112 Angle : 0.580 11.497 17210 Z= 0.290 Chirality : 0.043 0.248 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.239 108.848 1830 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.50 % Allowed : 14.57 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.34 (0.21), residues: 1612 helix: 0.07 (0.20), residues: 721 sheet: -0.80 (0.47), residues: 145 loop : -1.88 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 129 TYR 0.013 0.001 TYR D 354 PHE 0.009 0.001 PHE A 165 TRP 0.009 0.001 TRP A 398 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00259 (12620) covalent geometry : angle 0.58037 (17210) hydrogen bonds : bond 0.03492 ( 464) hydrogen bonds : angle 4.38020 ( 1353) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.522 Fit side-chains REVERT: A 85 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7541 (mp0) REVERT: B 28 PHE cc_start: 0.7420 (t80) cc_final: 0.7198 (t80) REVERT: B 68 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7263 (ttm-80) REVERT: B 95 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8280 (t80) REVERT: B 185 MET cc_start: 0.8475 (tpt) cc_final: 0.7835 (mpp) REVERT: B 215 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8194 (pp) REVERT: C 112 TRP cc_start: 0.7910 (t60) cc_final: 0.7098 (t-100) REVERT: C 175 ASP cc_start: 0.8842 (p0) cc_final: 0.8600 (p0) REVERT: C 276 ASP cc_start: 0.8386 (m-30) cc_final: 0.8016 (m-30) REVERT: D 404 ARG cc_start: 0.7226 (mmt180) cc_final: 0.6756 (mtm-85) REVERT: D 430 ARG cc_start: 0.9133 (ttp80) cc_final: 0.8897 (ptm-80) outliers start: 19 outliers final: 16 residues processed: 118 average time/residue: 0.1361 time to fit residues: 22.3739 Evaluate side-chains 116 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 61 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 148 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.081844 restraints weight = 20883.195| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.34 r_work: 0.2823 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12622 Z= 0.101 Angle : 0.572 11.535 17210 Z= 0.288 Chirality : 0.042 0.172 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.129 109.159 1830 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.57 % Allowed : 14.65 % Favored : 83.78 % 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: -1.17 (0.22), residues: 1612 helix: 0.20 (0.20), residues: 724 sheet: -0.72 (0.47), residues: 145 loop : -1.78 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 129 TYR 0.011 0.001 TYR C 176 PHE 0.008 0.001 PHE B 145 TRP 0.009 0.001 TRP A 518 HIS 0.006 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00225 (12620) covalent geometry : angle 0.57178 (17210) hydrogen bonds : bond 0.03314 ( 464) hydrogen bonds : angle 4.30971 ( 1353) Misc. bond : bond 0.00009 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 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: 20 poor density : 108 time to evaluate : 0.528 Fit side-chains REVERT: A 85 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7585 (mp0) REVERT: B 28 PHE cc_start: 0.7437 (t80) cc_final: 0.7206 (t80) REVERT: B 68 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7250 (ttm-80) REVERT: B 95 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8307 (t80) REVERT: B 185 MET cc_start: 0.8453 (tpt) cc_final: 0.7751 (mmm) REVERT: C 112 TRP cc_start: 0.7885 (t60) cc_final: 0.7100 (t-100) REVERT: C 175 ASP cc_start: 0.8830 (p0) cc_final: 0.8610 (p0) REVERT: C 276 ASP cc_start: 0.8424 (m-30) cc_final: 0.8053 (m-30) REVERT: D 404 ARG cc_start: 0.7145 (mmt180) cc_final: 0.6779 (mtm-85) REVERT: D 430 ARG cc_start: 0.9156 (ttp80) cc_final: 0.8934 (ptm-80) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.1300 time to fit residues: 22.0663 Evaluate side-chains 121 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 497 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.081599 restraints weight = 20788.860| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.33 r_work: 0.2818 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12622 Z= 0.113 Angle : 0.587 12.576 17210 Z= 0.292 Chirality : 0.043 0.172 2004 Planarity : 0.004 0.063 2239 Dihedral : 7.077 109.203 1830 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.57 % Allowed : 14.57 % Favored : 83.86 % 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: -1.10 (0.22), residues: 1612 helix: 0.26 (0.20), residues: 722 sheet: -0.70 (0.48), residues: 145 loop : -1.75 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 286 TYR 0.013 0.001 TYR D 354 PHE 0.008 0.001 PHE A 165 TRP 0.009 0.001 TRP A 518 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00261 (12620) covalent geometry : angle 0.58718 (17210) hydrogen bonds : bond 0.03390 ( 464) hydrogen bonds : angle 4.29087 ( 1353) Misc. bond : bond 0.00011 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2846.48 seconds wall clock time: 49 minutes 26.34 seconds (2966.34 seconds total)