Starting phenix.real_space_refine on Thu Mar 5 15:00:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i5z_52643/03_2026/9i5z_52643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i5z_52643/03_2026/9i5z_52643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i5z_52643/03_2026/9i5z_52643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i5z_52643/03_2026/9i5z_52643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i5z_52643/03_2026/9i5z_52643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i5z_52643/03_2026/9i5z_52643.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 7462 2.51 5 N 1807 2.21 5 O 1979 1.98 5 H 11386 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22682 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7542 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 12, 'TRANS': 484} Chain breaks: 2 Chain: "B" Number of atoms: 7615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7615 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 12, 'TRANS': 487} Chain breaks: 2 Chain: "C" Number of atoms: 7525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7525 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 12, 'TRANS': 482} Chain breaks: 2 Time building chain proxies: 3.90, per 1000 atoms: 0.17 Number of scatterers: 22682 At special positions: 0 Unit cell: (80.4882, 113.63, 108.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1979 8.00 N 1807 7.00 C 7462 6.00 H 11386 1.00 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=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 792.4 milliseconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 59 through 80 Proline residue: A 65 - end of helix removed outlier: 3.655A pdb=" N ILE A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 120 removed outlier: 3.622A pdb=" N ASP A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.917A pdb=" N THR A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.702A pdb=" N MET A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.555A pdb=" N HIS A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 232 removed outlier: 6.853A pdb=" N GLU A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 269 removed outlier: 4.058A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.977A pdb=" N SER A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 324 removed outlier: 4.009A pdb=" N MET A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 331 through 343 removed outlier: 3.911A pdb=" N GLY A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.526A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 389 Proline residue: A 379 - end of helix removed outlier: 3.522A pdb=" N ILE A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 426 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 439 through 447 removed outlier: 3.795A pdb=" N LEU A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 481 Processing helix chain 'A' and resid 488 through 511 removed outlier: 4.025A pdb=" N GLY A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 525 removed outlier: 3.689A pdb=" N ILE A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 546 removed outlier: 3.796A pdb=" N PHE A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'B' and resid 59 through 79 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 83 through 120 removed outlier: 4.234A pdb=" N ASP B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.551A pdb=" N MET B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 210 removed outlier: 3.873A pdb=" N VAL B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 232 removed outlier: 7.592A pdb=" N GLU B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 268 removed outlier: 3.600A pdb=" N PHE B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 removed outlier: 4.406A pdb=" N GLY B 281 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 324 removed outlier: 3.765A pdb=" N MET B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 331 through 343 removed outlier: 3.581A pdb=" N ILE B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.574A pdb=" N SER B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 388 removed outlier: 3.725A pdb=" N TYR B 370 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) Proline residue: B 379 - end of helix removed outlier: 4.466A pdb=" N MET B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 403 through 426 removed outlier: 3.527A pdb=" N ALA B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.703A pdb=" N GLY B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 454 through 481 removed outlier: 3.602A pdb=" N MET B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 511 removed outlier: 3.643A pdb=" N LEU B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.500A pdb=" N ASN B 517 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 546 removed outlier: 3.807A pdb=" N VAL B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 541 " --> pdb=" O MET B 537 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 Processing helix chain 'C' and resid 59 through 80 Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 80 through 120 removed outlier: 3.630A pdb=" N ALA C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.523A pdb=" N PHE C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 168 removed outlier: 3.644A pdb=" N MET C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR C 159 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix removed outlier: 3.580A pdb=" N TYR C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 4.129A pdb=" N HIS C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.611A pdb=" N TYR C 197 " --> pdb=" O PRO C 193 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 232 through 268 removed outlier: 3.974A pdb=" N LYS C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N CYS C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 4.307A pdb=" N VAL C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 296 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 324 removed outlier: 3.645A pdb=" N MET C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA C 314 " --> pdb=" O MET C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 343 removed outlier: 4.171A pdb=" N GLY C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 349 removed outlier: 3.557A pdb=" N GLY C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 366 through 388 removed outlier: 3.642A pdb=" N SER C 378 " --> pdb=" O TRP C 374 " (cutoff:3.500A) Proline residue: C 379 - end of helix removed outlier: 4.200A pdb=" N MET C 383 " --> pdb=" O PRO C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 403 removed outlier: 3.827A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 426 removed outlier: 3.760A pdb=" N VAL C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 418 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 423 " --> pdb=" O THR C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 450 through 481 removed outlier: 4.374A pdb=" N ILE C 455 " --> pdb=" O GLN C 451 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 456 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 475 " --> pdb=" O SER C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 509 Processing helix chain 'C' and resid 513 through 527 removed outlier: 3.832A pdb=" N ASN C 517 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 518 " --> pdb=" O ALA C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 545 removed outlier: 4.102A pdb=" N PHE C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL C 541 " --> pdb=" O MET C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 557 837 hydrogen bonds defined for protein. 2490 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: 5.53 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11383 1.03 - 1.23: 8 1.23 - 1.42: 4958 1.42 - 1.62: 6529 1.62 - 1.81: 93 Bond restraints: 22971 Sorted by residual: bond pdb=" C GLU C 161 " pdb=" N PRO C 162 " ideal model delta sigma weight residual 1.335 1.300 0.035 1.19e-02 7.06e+03 8.50e+00 bond pdb=" C GLU C 161 " pdb=" O GLU C 161 " ideal model delta sigma weight residual 1.238 1.204 0.034 1.28e-02 6.10e+03 7.06e+00 bond pdb=" CA GLU C 161 " pdb=" C GLU C 161 " ideal model delta sigma weight residual 1.524 1.549 -0.026 1.26e-02 6.30e+03 4.11e+00 bond pdb=" CA VAL C 64 " pdb=" CB VAL C 64 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 1.99e+00 bond pdb=" N GLU C 161 " pdb=" CA GLU C 161 " ideal model delta sigma weight residual 1.457 1.475 -0.019 1.41e-02 5.03e+03 1.73e+00 ... (remaining 22966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 40500 1.61 - 3.22: 866 3.22 - 4.82: 59 4.82 - 6.43: 17 6.43 - 8.04: 2 Bond angle restraints: 41444 Sorted by residual: angle pdb=" C GLU C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta sigma weight residual 119.56 115.94 3.62 1.02e+00 9.61e-01 1.26e+01 angle pdb=" N VAL A 62 " pdb=" CA VAL A 62 " pdb=" C VAL A 62 " ideal model delta sigma weight residual 111.90 109.14 2.76 8.10e-01 1.52e+00 1.16e+01 angle pdb=" CA TRP C 377 " pdb=" CB TRP C 377 " pdb=" CG TRP C 377 " ideal model delta sigma weight residual 113.60 118.83 -5.23 1.90e+00 2.77e-01 7.58e+00 angle pdb=" CA LEU C 241 " pdb=" CB LEU C 241 " pdb=" CG LEU C 241 " ideal model delta sigma weight residual 116.30 124.11 -7.81 3.50e+00 8.16e-02 4.98e+00 angle pdb=" CB MET B 453 " pdb=" CG MET B 453 " pdb=" SD MET B 453 " ideal model delta sigma weight residual 112.70 118.89 -6.19 3.00e+00 1.11e-01 4.25e+00 ... (remaining 41439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 9368 17.41 - 34.82: 907 34.82 - 52.22: 271 52.22 - 69.63: 164 69.63 - 87.04: 85 Dihedral angle restraints: 10795 sinusoidal: 5576 harmonic: 5219 Sorted by residual: dihedral pdb=" CA LEU C 402 " pdb=" C LEU C 402 " pdb=" N LEU C 403 " pdb=" CA LEU C 403 " ideal model delta harmonic sigma weight residual 180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA TRP B 366 " pdb=" C TRP B 366 " pdb=" N THR B 367 " pdb=" CA THR B 367 " ideal model delta harmonic sigma weight residual 180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU C 428 " pdb=" CG GLU C 428 " pdb=" CD GLU C 428 " pdb=" OE1 GLU C 428 " ideal model delta sinusoidal sigma weight residual 0.00 -87.04 87.04 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 10792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1120 0.027 - 0.053: 465 0.053 - 0.080: 197 0.080 - 0.106: 53 0.106 - 0.133: 17 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA VAL B 280 " pdb=" N VAL B 280 " pdb=" C VAL B 280 " pdb=" CB VAL B 280 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA PRO B 379 " pdb=" N PRO B 379 " pdb=" C PRO B 379 " pdb=" CB PRO B 379 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA VAL B 170 " pdb=" N VAL B 170 " pdb=" C VAL B 170 " pdb=" CB VAL B 170 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 1849 not shown) Planarity restraints: 3378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 222 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO B 223 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 404 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 405 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 405 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 405 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 333 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO C 334 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " -0.025 5.00e-02 4.00e+02 ... (remaining 3375 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 2762 2.27 - 2.85: 52119 2.85 - 3.43: 62806 3.43 - 4.02: 84897 4.02 - 4.60: 131610 Nonbonded interactions: 334194 Sorted by model distance: nonbonded pdb=" O LEU B 363 " pdb=" H ILE B 368 " model vdw 1.686 2.450 nonbonded pdb=" O TRP C 373 " pdb=" HG SER C 376 " model vdw 1.712 2.450 nonbonded pdb=" OE1 GLU A 161 " pdb=" HE1 TRP A 189 " model vdw 1.713 2.450 nonbonded pdb=" O THR C 160 " pdb=" H THR C 164 " model vdw 1.714 2.450 nonbonded pdb=" O MET A 186 " pdb=" HG1 THR A 190 " model vdw 1.715 2.450 ... (remaining 334189 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 296 or resid 301 through 557)) selection = (chain 'B' and (resid 56 through 296 or resid 301 through 555 or (resid 556 thro \ ugh 557 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)))) selection = (chain 'C' and (resid 56 through 555 or (resid 556 through 557 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name N \ E2)))) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.070 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 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 : 0.004 0.050 11585 Z= 0.157 Angle : 0.560 8.041 15795 Z= 0.294 Chirality : 0.036 0.133 1852 Planarity : 0.004 0.062 1934 Dihedral : 12.994 87.038 3812 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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 are not related in a simple way. whole: -1.24 (0.21), residues: 1474 helix: -0.67 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.007 0.001 TYR B 340 PHE 0.013 0.001 PHE B 464 TRP 0.027 0.002 TRP B 371 HIS 0.008 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00374 (11585) covalent geometry : angle 0.56033 (15795) hydrogen bonds : bond 0.27365 ( 837) hydrogen bonds : angle 10.20299 ( 2490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 ILE cc_start: 0.7807 (mt) cc_final: 0.7597 (mt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2082 time to fit residues: 66.9960 Evaluate side-chains 149 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 339 ASN B 439 GLN B 517 ASN C 59 ASN C 519 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.116477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.092247 restraints weight = 78125.916| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.17 r_work: 0.3515 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11585 Z= 0.232 Angle : 0.626 5.294 15795 Z= 0.360 Chirality : 0.038 0.131 1852 Planarity : 0.005 0.043 1934 Dihedral : 4.343 19.902 1548 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.89 % Allowed : 7.92 % Favored : 90.18 % 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 are not related in a simple way. whole: -0.21 (0.21), residues: 1474 helix: 0.17 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -0.76 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.013 0.001 TYR A 157 PHE 0.015 0.002 PHE B 113 TRP 0.014 0.001 TRP B 194 HIS 0.006 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00463 (11585) covalent geometry : angle 0.62555 (15795) hydrogen bonds : bond 0.06002 ( 837) hydrogen bonds : angle 6.08685 ( 2490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.8551 (mmm) cc_final: 0.8333 (mmm) REVERT: B 84 PHE cc_start: 0.8373 (t80) cc_final: 0.7891 (t80) REVERT: C 399 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7961 (mp) outliers start: 22 outliers final: 16 residues processed: 167 average time/residue: 0.1883 time to fit residues: 48.2221 Evaluate side-chains 156 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 536 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 0.0070 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.116768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.092638 restraints weight = 77774.568| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.19 r_work: 0.3522 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11585 Z= 0.175 Angle : 0.544 7.592 15795 Z= 0.304 Chirality : 0.036 0.157 1852 Planarity : 0.004 0.041 1934 Dihedral : 4.159 20.030 1548 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.72 % Allowed : 10.59 % Favored : 87.68 % 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 are not related in a simple way. whole: 0.29 (0.21), residues: 1474 helix: 0.55 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.78 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.012 0.001 TYR A 304 PHE 0.021 0.001 PHE A 465 TRP 0.017 0.001 TRP B 495 HIS 0.005 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00361 (11585) covalent geometry : angle 0.54353 (15795) hydrogen bonds : bond 0.05049 ( 837) hydrogen bonds : angle 5.47124 ( 2490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.7956 (t0) cc_final: 0.7637 (t0) REVERT: A 353 MET cc_start: 0.8609 (mmm) cc_final: 0.8389 (mmm) REVERT: A 505 THR cc_start: 0.7896 (m) cc_final: 0.7627 (m) REVERT: B 144 MET cc_start: 0.8487 (tpt) cc_final: 0.8226 (tpt) REVERT: C 160 THR cc_start: 0.7898 (p) cc_final: 0.7630 (m) REVERT: C 399 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7958 (mp) REVERT: C 458 MET cc_start: 0.8472 (mtm) cc_final: 0.7927 (mtp) REVERT: C 476 MET cc_start: 0.8519 (mtt) cc_final: 0.8245 (mpp) outliers start: 20 outliers final: 17 residues processed: 166 average time/residue: 0.1884 time to fit residues: 48.7472 Evaluate side-chains 153 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.114458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.090135 restraints weight = 79390.923| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.20 r_work: 0.3474 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11585 Z= 0.287 Angle : 0.602 6.814 15795 Z= 0.345 Chirality : 0.039 0.131 1852 Planarity : 0.004 0.047 1934 Dihedral : 4.269 18.277 1548 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.84 % Allowed : 11.80 % Favored : 85.36 % 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 are not related in a simple way. whole: 0.17 (0.21), residues: 1474 helix: 0.51 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.014 0.002 TYR A 304 PHE 0.017 0.002 PHE A 465 TRP 0.027 0.002 TRP B 495 HIS 0.007 0.002 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00607 (11585) covalent geometry : angle 0.60208 (15795) hydrogen bonds : bond 0.04810 ( 837) hydrogen bonds : angle 5.41161 ( 2490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.7977 (t0) cc_final: 0.7652 (t0) REVERT: A 505 THR cc_start: 0.7929 (m) cc_final: 0.7657 (m) REVERT: C 399 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 458 MET cc_start: 0.8535 (mtm) cc_final: 0.8067 (mtp) outliers start: 33 outliers final: 26 residues processed: 165 average time/residue: 0.1823 time to fit residues: 47.5220 Evaluate side-chains 161 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.115986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091721 restraints weight = 77400.701| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.22 r_work: 0.3515 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11585 Z= 0.152 Angle : 0.510 5.342 15795 Z= 0.285 Chirality : 0.036 0.150 1852 Planarity : 0.003 0.043 1934 Dihedral : 4.094 16.030 1548 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.33 % Allowed : 12.40 % Favored : 85.27 % 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 are not related in a simple way. whole: 0.67 (0.22), residues: 1474 helix: 0.87 (0.15), residues: 1153 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.014 0.001 TYR A 304 PHE 0.020 0.001 PHE A 465 TRP 0.024 0.001 TRP B 495 HIS 0.004 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00315 (11585) covalent geometry : angle 0.50986 (15795) hydrogen bonds : bond 0.04218 ( 837) hydrogen bonds : angle 5.04538 ( 2490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.7880 (t0) cc_final: 0.7533 (t0) REVERT: A 505 THR cc_start: 0.7909 (m) cc_final: 0.7645 (m) REVERT: C 399 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7942 (mp) REVERT: C 458 MET cc_start: 0.8456 (mtm) cc_final: 0.8139 (mtp) REVERT: C 479 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8425 (mpp) outliers start: 27 outliers final: 23 residues processed: 165 average time/residue: 0.1838 time to fit residues: 47.7694 Evaluate side-chains 163 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.114427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090058 restraints weight = 78690.264| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.18 r_work: 0.3483 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11585 Z= 0.234 Angle : 0.554 5.307 15795 Z= 0.315 Chirality : 0.037 0.140 1852 Planarity : 0.004 0.046 1934 Dihedral : 4.138 15.708 1548 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.67 % Allowed : 12.66 % Favored : 84.67 % 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 are not related in a simple way. whole: 0.58 (0.22), residues: 1474 helix: 0.82 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.93 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 210 TYR 0.015 0.001 TYR A 304 PHE 0.034 0.002 PHE B 413 TRP 0.030 0.002 TRP B 495 HIS 0.007 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00497 (11585) covalent geometry : angle 0.55401 (15795) hydrogen bonds : bond 0.04312 ( 837) hydrogen bonds : angle 5.08730 ( 2490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 307 ASN cc_start: 0.7966 (t0) cc_final: 0.7537 (m-40) REVERT: A 505 THR cc_start: 0.7922 (m) cc_final: 0.7657 (m) REVERT: B 144 MET cc_start: 0.8315 (tpt) cc_final: 0.8088 (tpt) REVERT: C 458 MET cc_start: 0.8502 (mtm) cc_final: 0.8214 (mtp) REVERT: C 479 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8482 (mpp) outliers start: 31 outliers final: 26 residues processed: 163 average time/residue: 0.1731 time to fit residues: 44.9629 Evaluate side-chains 164 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.114906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.090551 restraints weight = 78389.317| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.22 r_work: 0.3494 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11585 Z= 0.185 Angle : 0.525 6.645 15795 Z= 0.294 Chirality : 0.036 0.159 1852 Planarity : 0.004 0.044 1934 Dihedral : 4.061 15.648 1548 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.76 % Allowed : 13.26 % Favored : 83.98 % 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 are not related in a simple way. whole: 0.79 (0.22), residues: 1474 helix: 0.96 (0.15), residues: 1157 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.015 0.001 TYR A 304 PHE 0.023 0.001 PHE B 413 TRP 0.035 0.001 TRP B 495 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00391 (11585) covalent geometry : angle 0.52489 (15795) hydrogen bonds : bond 0.04050 ( 837) hydrogen bonds : angle 4.93065 ( 2490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.7960 (t0) cc_final: 0.7523 (m-40) REVERT: A 505 THR cc_start: 0.7885 (m) cc_final: 0.7624 (m) REVERT: C 260 GLN cc_start: 0.5800 (OUTLIER) cc_final: 0.5460 (tt0) REVERT: C 399 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7993 (mp) REVERT: C 458 MET cc_start: 0.8451 (mtm) cc_final: 0.8228 (mtp) REVERT: C 479 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8507 (mpp) REVERT: C 527 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7288 (m) outliers start: 32 outliers final: 21 residues processed: 166 average time/residue: 0.1809 time to fit residues: 47.8978 Evaluate side-chains 161 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 42 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.115248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091167 restraints weight = 78277.434| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.18 r_work: 0.3519 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11585 Z= 0.155 Angle : 0.501 7.173 15795 Z= 0.279 Chirality : 0.035 0.161 1852 Planarity : 0.003 0.045 1934 Dihedral : 3.962 15.794 1548 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.24 % Allowed : 14.13 % Favored : 83.63 % 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 are not related in a simple way. whole: 1.06 (0.22), residues: 1474 helix: 1.17 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.82 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.015 0.001 TYR A 304 PHE 0.019 0.001 PHE B 413 TRP 0.018 0.001 TRP B 495 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00324 (11585) covalent geometry : angle 0.50074 (15795) hydrogen bonds : bond 0.03838 ( 837) hydrogen bonds : angle 4.78869 ( 2490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.7954 (t0) cc_final: 0.7533 (m-40) REVERT: A 505 THR cc_start: 0.7949 (m) cc_final: 0.7695 (m) REVERT: C 399 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8034 (mp) REVERT: C 458 MET cc_start: 0.8460 (mtm) cc_final: 0.8235 (mtp) REVERT: C 479 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8441 (mpp) REVERT: C 527 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7367 (m) outliers start: 26 outliers final: 20 residues processed: 161 average time/residue: 0.1821 time to fit residues: 46.4029 Evaluate side-chains 162 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 145 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.113712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.089560 restraints weight = 79116.951| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.20 r_work: 0.3485 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11585 Z= 0.245 Angle : 0.562 7.616 15795 Z= 0.317 Chirality : 0.038 0.158 1852 Planarity : 0.004 0.047 1934 Dihedral : 4.099 15.920 1548 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.24 % Allowed : 14.30 % Favored : 83.46 % 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 are not related in a simple way. whole: 0.76 (0.22), residues: 1474 helix: 0.95 (0.15), residues: 1157 sheet: None (None), residues: 0 loop : -0.91 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.017 0.002 TYR A 304 PHE 0.027 0.002 PHE B 413 TRP 0.021 0.002 TRP A 371 HIS 0.007 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00518 (11585) covalent geometry : angle 0.56208 (15795) hydrogen bonds : bond 0.04133 ( 837) hydrogen bonds : angle 4.95665 ( 2490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8593 (mmt) cc_final: 0.8337 (mmt) REVERT: A 307 ASN cc_start: 0.7969 (t0) cc_final: 0.7522 (m-40) REVERT: A 505 THR cc_start: 0.7879 (m) cc_final: 0.7622 (m) REVERT: C 260 GLN cc_start: 0.5679 (OUTLIER) cc_final: 0.5323 (tt0) REVERT: C 399 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7949 (mp) REVERT: C 458 MET cc_start: 0.8464 (mtm) cc_final: 0.8227 (mtp) REVERT: C 479 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8549 (mpp) REVERT: C 527 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7381 (m) outliers start: 26 outliers final: 20 residues processed: 158 average time/residue: 0.1784 time to fit residues: 44.8726 Evaluate side-chains 157 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 103 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.114828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.090774 restraints weight = 78595.483| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.21 r_work: 0.3506 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11585 Z= 0.161 Angle : 0.519 8.575 15795 Z= 0.286 Chirality : 0.036 0.162 1852 Planarity : 0.003 0.047 1934 Dihedral : 3.993 15.767 1548 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.81 % Allowed : 14.99 % Favored : 83.20 % 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 are not related in a simple way. whole: 1.08 (0.22), residues: 1474 helix: 1.18 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.016 0.001 TYR A 304 PHE 0.019 0.001 PHE A 465 TRP 0.019 0.001 TRP A 371 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00338 (11585) covalent geometry : angle 0.51868 (15795) hydrogen bonds : bond 0.03808 ( 837) hydrogen bonds : angle 4.77118 ( 2490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8567 (mmt) cc_final: 0.8310 (mmt) REVERT: A 307 ASN cc_start: 0.7948 (t0) cc_final: 0.7609 (t0) REVERT: A 479 MET cc_start: 0.7528 (mtp) cc_final: 0.7167 (mtm) REVERT: A 505 THR cc_start: 0.7945 (m) cc_final: 0.7704 (m) REVERT: C 127 LEU cc_start: 0.8957 (mt) cc_final: 0.8395 (tt) REVERT: C 399 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 479 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8508 (mpp) REVERT: C 527 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7360 (m) outliers start: 21 outliers final: 17 residues processed: 152 average time/residue: 0.1717 time to fit residues: 41.6021 Evaluate side-chains 154 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 527 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 33 optimal weight: 0.0370 chunk 140 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.114776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.090749 restraints weight = 78862.722| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.22 r_work: 0.3513 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11585 Z= 0.163 Angle : 0.518 8.442 15795 Z= 0.284 Chirality : 0.036 0.163 1852 Planarity : 0.003 0.048 1934 Dihedral : 3.936 15.614 1548 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.89 % Allowed : 15.16 % Favored : 82.95 % 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 are not related in a simple way. whole: 1.18 (0.22), residues: 1474 helix: 1.25 (0.15), residues: 1157 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.016 0.001 TYR A 304 PHE 0.019 0.001 PHE A 465 TRP 0.018 0.001 TRP C 490 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00345 (11585) covalent geometry : angle 0.51757 (15795) hydrogen bonds : bond 0.03729 ( 837) hydrogen bonds : angle 4.71608 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4609.78 seconds wall clock time: 78 minutes 49.19 seconds (4729.19 seconds total)