Starting phenix.real_space_refine on Sun May 3 14:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pwa_71905/05_2026/9pwa_71905.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pwa_71905/05_2026/9pwa_71905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pwa_71905/05_2026/9pwa_71905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pwa_71905/05_2026/9pwa_71905.map" model { file = "/net/cci-nas-00/data/ceres_data/9pwa_71905/05_2026/9pwa_71905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pwa_71905/05_2026/9pwa_71905.cif" } resolution = 2.55 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= 0.003 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8767 2.51 5 N 2336 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13707 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4737 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 22, 'TRANS': 577} Chain: "B" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4578 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 552} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3192 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 378} Chain breaks: 3 Chain: "S" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1200 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'TRANS': 141} Time building chain proxies: 2.89, per 1000 atoms: 0.21 Number of scatterers: 13707 At special positions: 0 Unit cell: (101.966, 110.376, 125.093, 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 72 16.00 O 2532 8.00 N 2336 7.00 C 8767 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=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 612.8 milliseconds 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 64.4% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 51 through 69 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.985A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 149 through 157 removed outlier: 4.067A pdb=" N LYS A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 218 removed outlier: 4.181A pdb=" N LYS A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.669A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 4.048A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.723A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 4.160A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.549A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.919A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 416 removed outlier: 4.364A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 436 removed outlier: 3.813A pdb=" N ARG A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.532A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.607A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 4.109A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.541A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 591 through 599 Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.696A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 62 through 80 removed outlier: 4.200A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.598A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 removed outlier: 3.892A pdb=" N LYS B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.670A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.813A pdb=" N TYR B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.854A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.882A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 168 Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.873A pdb=" N ASN B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 214 removed outlier: 4.053A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.526A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.771A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.923A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.521A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.585A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.855A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.598A pdb=" N LEU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.642A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 535 through 542 removed outlier: 3.514A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.828A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 125 through 133 removed outlier: 4.917A pdb=" N THR M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 41 removed outlier: 3.932A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19 removed outlier: 3.617A pdb=" N ILE M 16 " --> pdb=" O ILE M 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248 removed outlier: 5.427A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA M 350 " --> pdb=" O LYS M 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 253 through 254 removed outlier: 6.634A pdb=" N GLU M 211 " --> pdb=" O VAL M 406 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL M 406 " --> pdb=" O GLU M 211 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS M 213 " --> pdb=" O LEU M 404 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU M 404 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY M 215 " --> pdb=" O ARG M 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 287 through 294 removed outlier: 8.462A pdb=" N GLN M 365 " --> pdb=" O CYS M 337 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N CYS M 337 " --> pdb=" O GLN M 365 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER M 367 " --> pdb=" O VAL M 335 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL M 335 " --> pdb=" O SER M 367 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU M 369 " --> pdb=" O VAL M 333 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL M 333 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU M 371 " --> pdb=" O SER M 331 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.176A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 118 through 119 817 hydrogen bonds defined for protein. 2376 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: 1.70 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4473 1.34 - 1.46: 2262 1.46 - 1.58: 7104 1.58 - 1.70: 1 1.70 - 1.81: 111 Bond restraints: 13951 Sorted by residual: bond pdb=" CA PHE B 581 " pdb=" CB PHE B 581 " ideal model delta sigma weight residual 1.527 1.580 -0.053 2.48e-02 1.63e+03 4.57e+00 bond pdb=" CG PRO A 294 " pdb=" CD PRO A 294 " ideal model delta sigma weight residual 1.503 1.432 0.071 3.40e-02 8.65e+02 4.36e+00 bond pdb=" N PRO A 294 " pdb=" CA PRO A 294 " ideal model delta sigma weight residual 1.459 1.480 -0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" C PHE B 51 " pdb=" N PRO B 52 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 2.02e+00 bond pdb=" CB ARG A 341 " pdb=" CG ARG A 341 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 ... (remaining 13946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 18654 2.41 - 4.83: 214 4.83 - 7.24: 11 7.24 - 9.66: 6 9.66 - 12.07: 1 Bond angle restraints: 18886 Sorted by residual: angle pdb=" N ASN B 179 " pdb=" CA ASN B 179 " pdb=" C ASN B 179 " ideal model delta sigma weight residual 114.62 106.97 7.65 1.14e+00 7.69e-01 4.51e+01 angle pdb=" N PRO A 294 " pdb=" CD PRO A 294 " pdb=" CG PRO A 294 " ideal model delta sigma weight residual 103.20 93.99 9.21 1.50e+00 4.44e-01 3.77e+01 angle pdb=" CA PRO A 294 " pdb=" N PRO A 294 " pdb=" CD PRO A 294 " ideal model delta sigma weight residual 112.00 105.07 6.93 1.40e+00 5.10e-01 2.45e+01 angle pdb=" N PRO A 294 " pdb=" CA PRO A 294 " pdb=" CB PRO A 294 " ideal model delta sigma weight residual 103.22 100.83 2.39 5.20e-01 3.70e+00 2.12e+01 angle pdb=" CA PRO A 294 " pdb=" CB PRO A 294 " pdb=" CG PRO A 294 " ideal model delta sigma weight residual 104.50 96.16 8.34 1.90e+00 2.77e-01 1.93e+01 ... (remaining 18881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 7267 17.63 - 35.25: 912 35.25 - 52.87: 303 52.87 - 70.50: 66 70.50 - 88.12: 32 Dihedral angle restraints: 8580 sinusoidal: 3488 harmonic: 5092 Sorted by residual: dihedral pdb=" CA ARG A 472 " pdb=" C ARG A 472 " pdb=" N ASP A 473 " pdb=" CA ASP A 473 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA HIS A 493 " pdb=" C HIS A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASN A 401 " pdb=" C ASN A 401 " pdb=" N ALA A 402 " pdb=" CA ALA A 402 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1333 0.032 - 0.064: 607 0.064 - 0.096: 174 0.096 - 0.127: 73 0.127 - 0.159: 11 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CB ILE A 420 " pdb=" CA ILE A 420 " pdb=" CG1 ILE A 420 " pdb=" CG2 ILE A 420 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA PRO B 271 " pdb=" N PRO B 271 " pdb=" C PRO B 271 " pdb=" CB PRO B 271 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA MET B 155 " pdb=" N MET B 155 " pdb=" C MET B 155 " pdb=" CB MET B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2195 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 602 " 0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO A 603 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 603 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 603 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 245 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO B 246 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR M 120 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO M 121 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO M 121 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO M 121 " -0.026 5.00e-02 4.00e+02 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 292 2.70 - 3.25: 13074 3.25 - 3.80: 21333 3.80 - 4.35: 28201 4.35 - 4.90: 47026 Nonbonded interactions: 109926 Sorted by model distance: nonbonded pdb=" O ASP A 198 " pdb=" NH2 ARG A 232 " model vdw 2.150 3.120 nonbonded pdb=" O PRO M 327 " pdb=" OG1 THR M 330 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR B 136 " pdb=" OE2 GLU M 114 " model vdw 2.192 3.040 nonbonded pdb=" NH2 ARG A 263 " pdb=" O ASN S 74 " model vdw 2.203 3.120 nonbonded pdb=" OE2 GLU A 107 " pdb=" NH2 ARG A 110 " model vdw 2.226 3.120 ... (remaining 109921 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: 0.010 Normalize map: mean=0, sd=1: 0.480 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.003 0.071 13951 Z= 0.165 Angle : 0.691 12.074 18886 Z= 0.430 Chirality : 0.041 0.159 2198 Planarity : 0.005 0.086 2403 Dihedral : 18.457 88.124 5262 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 1.31 % Allowed : 23.92 % Favored : 74.77 % 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: 0.91 (0.20), residues: 1703 helix: 1.42 (0.16), residues: 1013 sheet: 0.88 (0.39), residues: 177 loop : -1.14 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 472 TYR 0.020 0.002 TYR B 276 PHE 0.015 0.001 PHE M 93 TRP 0.014 0.002 TRP M 381 HIS 0.006 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00339 (13951) covalent geometry : angle 0.69120 (18886) hydrogen bonds : bond 0.13096 ( 817) hydrogen bonds : angle 5.23378 ( 2376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 380 time to evaluate : 0.456 Fit side-chains REVERT: A 522 GLN cc_start: 0.7357 (mt0) cc_final: 0.7139 (tt0) REVERT: B 82 ASP cc_start: 0.7546 (m-30) cc_final: 0.7287 (m-30) REVERT: B 169 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6378 (tt) REVERT: B 186 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7001 (tt0) REVERT: B 200 ASN cc_start: 0.5260 (m-40) cc_final: 0.4891 (p0) REVERT: B 212 ASN cc_start: 0.7770 (m110) cc_final: 0.7554 (m110) REVERT: B 340 ASP cc_start: 0.7623 (m-30) cc_final: 0.7416 (m-30) REVERT: B 464 GLU cc_start: 0.7022 (pm20) cc_final: 0.6494 (pm20) REVERT: B 521 ASP cc_start: 0.7232 (m-30) cc_final: 0.6775 (m-30) REVERT: M 9 ASN cc_start: 0.7765 (p0) cc_final: 0.7454 (p0) REVERT: M 85 MET cc_start: 0.7993 (ttp) cc_final: 0.7755 (ttm) REVERT: M 323 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7697 (ttt-90) REVERT: M 328 LEU cc_start: 0.8420 (mp) cc_final: 0.8218 (mt) REVERT: M 348 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6757 (mt-10) REVERT: M 369 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7296 (mt-10) REVERT: M 408 GLU cc_start: 0.7304 (tp30) cc_final: 0.6686 (tp30) REVERT: S 41 VAL cc_start: 0.8254 (p) cc_final: 0.8052 (t) REVERT: S 111 TYR cc_start: 0.8481 (m-80) cc_final: 0.8105 (m-80) outliers start: 20 outliers final: 11 residues processed: 396 average time/residue: 0.7724 time to fit residues: 326.6110 Evaluate side-chains 335 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 323 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain S residue 49 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 197 ASN A 200 HIS A 339 GLN A 448 ASN A 476 GLN A 522 GLN A 527 HIS A 560 GLN B 80 GLN B 152 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 353 GLN B 386 GLN B 461 ASN B 505 GLN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN M 100 ASN M 135 GLN M 136 GLN M 190 GLN S 36 HIS S 46 HIS S 48 ASN S 74 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116385 restraints weight = 18350.377| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.98 r_work: 0.3483 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13951 Z= 0.116 Angle : 0.525 6.857 18886 Z= 0.280 Chirality : 0.040 0.165 2198 Planarity : 0.004 0.067 2403 Dihedral : 5.372 74.527 1887 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 3.34 % Allowed : 23.85 % Favored : 72.80 % 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: 1.37 (0.20), residues: 1703 helix: 1.76 (0.16), residues: 1013 sheet: 1.16 (0.39), residues: 174 loop : -0.88 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 381 TYR 0.013 0.001 TYR B 72 PHE 0.010 0.001 PHE S 4 TRP 0.013 0.001 TRP A 462 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00249 (13951) covalent geometry : angle 0.52502 (18886) hydrogen bonds : bond 0.04183 ( 817) hydrogen bonds : angle 4.29843 ( 2376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 0.390 Fit side-chains REVERT: A 522 GLN cc_start: 0.7659 (mt0) cc_final: 0.7383 (tt0) REVERT: B 82 ASP cc_start: 0.7783 (m-30) cc_final: 0.7552 (m-30) REVERT: B 169 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6641 (tt) REVERT: B 186 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7528 (tt0) REVERT: B 200 ASN cc_start: 0.5533 (m-40) cc_final: 0.4994 (p0) REVERT: B 471 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: M 9 ASN cc_start: 0.8511 (p0) cc_final: 0.8237 (p0) REVERT: M 80 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7972 (mm-30) REVERT: M 179 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8117 (mt-10) REVERT: M 276 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7809 (ttp80) REVERT: M 310 ASN cc_start: 0.8227 (m110) cc_final: 0.7986 (m110) REVERT: M 408 GLU cc_start: 0.7603 (tp30) cc_final: 0.7299 (tm-30) REVERT: S 111 TYR cc_start: 0.8696 (m-80) cc_final: 0.8344 (m-80) outliers start: 51 outliers final: 17 residues processed: 351 average time/residue: 0.7732 time to fit residues: 289.6488 Evaluate side-chains 331 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 311 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 276 ARG Chi-restraints excluded: chain S residue 49 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 18 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: A 339 GLN B 80 GLN B 212 ASN B 386 GLN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN M 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.130998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115047 restraints weight = 18416.285| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.98 r_work: 0.3463 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13951 Z= 0.127 Angle : 0.506 5.781 18886 Z= 0.269 Chirality : 0.040 0.157 2198 Planarity : 0.004 0.062 2403 Dihedral : 4.582 46.551 1875 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 3.21 % Allowed : 24.90 % Favored : 71.89 % 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: 1.48 (0.20), residues: 1703 helix: 1.86 (0.16), residues: 1015 sheet: 1.26 (0.39), residues: 173 loop : -0.92 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 243 TYR 0.013 0.001 TYR M 8 PHE 0.014 0.001 PHE M 93 TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00293 (13951) covalent geometry : angle 0.50624 (18886) hydrogen bonds : bond 0.04259 ( 817) hydrogen bonds : angle 4.13441 ( 2376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 0.485 Fit side-chains REVERT: A 522 GLN cc_start: 0.7727 (mt0) cc_final: 0.7505 (mt0) REVERT: B 82 ASP cc_start: 0.7853 (m-30) cc_final: 0.7621 (m-30) REVERT: B 166 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8151 (ttm-80) REVERT: B 169 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6798 (tt) REVERT: B 186 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7644 (tt0) REVERT: B 200 ASN cc_start: 0.5388 (m-40) cc_final: 0.4882 (p0) REVERT: B 471 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: M 9 ASN cc_start: 0.8555 (p0) cc_final: 0.8322 (p0) REVERT: M 310 ASN cc_start: 0.8247 (m110) cc_final: 0.8012 (m110) REVERT: M 343 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8287 (ptpp) REVERT: M 408 GLU cc_start: 0.7653 (tp30) cc_final: 0.6978 (tp30) REVERT: S 111 TYR cc_start: 0.8663 (m-80) cc_final: 0.8379 (m-80) outliers start: 49 outliers final: 20 residues processed: 357 average time/residue: 0.7781 time to fit residues: 296.7718 Evaluate side-chains 343 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 321 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain S residue 49 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 164 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN B 80 GLN B 212 ASN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN M 122 GLN M 190 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115242 restraints weight = 18376.337| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.97 r_work: 0.3466 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13951 Z= 0.116 Angle : 0.488 5.319 18886 Z= 0.260 Chirality : 0.040 0.170 2198 Planarity : 0.004 0.058 2403 Dihedral : 4.484 47.771 1874 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 3.01 % Allowed : 25.10 % Favored : 71.89 % 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: 1.60 (0.21), residues: 1703 helix: 1.96 (0.16), residues: 1017 sheet: 1.18 (0.37), residues: 185 loop : -0.87 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 243 TYR 0.015 0.001 TYR B 72 PHE 0.013 0.001 PHE M 93 TRP 0.014 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00264 (13951) covalent geometry : angle 0.48815 (18886) hydrogen bonds : bond 0.03946 ( 817) hydrogen bonds : angle 4.04767 ( 2376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 324 time to evaluate : 0.436 Fit side-chains REVERT: A 123 ARG cc_start: 0.7306 (mmm160) cc_final: 0.7099 (mmm160) REVERT: A 522 GLN cc_start: 0.7718 (mt0) cc_final: 0.7419 (mt0) REVERT: B 82 ASP cc_start: 0.7838 (m-30) cc_final: 0.7582 (m-30) REVERT: B 167 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: B 186 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7629 (tt0) REVERT: B 200 ASN cc_start: 0.5370 (m-40) cc_final: 0.4866 (p0) REVERT: B 512 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.8005 (mm-40) REVERT: M 9 ASN cc_start: 0.8552 (p0) cc_final: 0.8326 (p0) REVERT: M 310 ASN cc_start: 0.8265 (m110) cc_final: 0.8019 (m110) REVERT: M 408 GLU cc_start: 0.7642 (tp30) cc_final: 0.6950 (tp30) REVERT: S 111 TYR cc_start: 0.8651 (m-80) cc_final: 0.8339 (m-80) outliers start: 46 outliers final: 23 residues processed: 345 average time/residue: 0.8012 time to fit residues: 294.8544 Evaluate side-chains 339 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 314 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain S residue 49 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.0040 chunk 132 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 212 ASN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116118 restraints weight = 18552.931| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.89 r_work: 0.3483 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13951 Z= 0.103 Angle : 0.482 10.491 18886 Z= 0.253 Chirality : 0.040 0.232 2198 Planarity : 0.004 0.055 2403 Dihedral : 4.303 48.981 1871 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 2.75 % Allowed : 26.02 % Favored : 71.23 % 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: 1.70 (0.21), residues: 1703 helix: 2.03 (0.16), residues: 1019 sheet: 1.26 (0.38), residues: 184 loop : -0.83 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 243 TYR 0.015 0.001 TYR B 72 PHE 0.011 0.001 PHE M 93 TRP 0.015 0.001 TRP A 462 HIS 0.007 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00225 (13951) covalent geometry : angle 0.48224 (18886) hydrogen bonds : bond 0.03615 ( 817) hydrogen bonds : angle 3.96563 ( 2376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 324 time to evaluate : 0.530 Fit side-chains REVERT: B 82 ASP cc_start: 0.7787 (m-30) cc_final: 0.7538 (m-30) REVERT: B 167 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: B 186 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7566 (tt0) REVERT: B 200 ASN cc_start: 0.5325 (m-40) cc_final: 0.4902 (p0) REVERT: M 9 ASN cc_start: 0.8581 (p0) cc_final: 0.8357 (p0) REVERT: M 77 MET cc_start: 0.8582 (ttm) cc_final: 0.8356 (ttp) REVERT: M 310 ASN cc_start: 0.8261 (m110) cc_final: 0.8027 (m110) REVERT: M 408 GLU cc_start: 0.7617 (tp30) cc_final: 0.6977 (tp30) REVERT: S 111 TYR cc_start: 0.8617 (m-80) cc_final: 0.8334 (m-80) outliers start: 42 outliers final: 23 residues processed: 344 average time/residue: 0.8115 time to fit residues: 297.8359 Evaluate side-chains 336 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 312 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain M residue 11 LYS Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 169 ARG Chi-restraints excluded: chain S residue 49 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 23 optimal weight: 10.0000 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN B 505 GLN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.115488 restraints weight = 18367.181| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.90 r_work: 0.3472 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13951 Z= 0.120 Angle : 0.496 11.390 18886 Z= 0.259 Chirality : 0.040 0.228 2198 Planarity : 0.004 0.052 2403 Dihedral : 4.288 48.787 1871 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 3.15 % Allowed : 25.56 % Favored : 71.30 % 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: 1.72 (0.21), residues: 1703 helix: 2.04 (0.16), residues: 1019 sheet: 1.30 (0.38), residues: 184 loop : -0.84 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 166 TYR 0.013 0.001 TYR B 276 PHE 0.013 0.001 PHE M 93 TRP 0.013 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00280 (13951) covalent geometry : angle 0.49563 (18886) hydrogen bonds : bond 0.03864 ( 817) hydrogen bonds : angle 3.99112 ( 2376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 322 time to evaluate : 0.537 Fit side-chains REVERT: B 82 ASP cc_start: 0.7858 (m-30) cc_final: 0.7638 (m-30) REVERT: B 167 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: B 186 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7621 (tt0) REVERT: B 200 ASN cc_start: 0.5335 (m-40) cc_final: 0.4907 (p0) REVERT: M 9 ASN cc_start: 0.8588 (p0) cc_final: 0.8387 (p0) REVERT: M 188 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7727 (mm-40) REVERT: M 310 ASN cc_start: 0.8263 (m110) cc_final: 0.8037 (m110) REVERT: M 343 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8321 (ptpp) REVERT: M 408 GLU cc_start: 0.7610 (tp30) cc_final: 0.7000 (tp30) REVERT: S 111 TYR cc_start: 0.8620 (m-80) cc_final: 0.8354 (m-80) REVERT: S 132 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8330 (mt) outliers start: 48 outliers final: 27 residues processed: 347 average time/residue: 0.8387 time to fit residues: 310.4111 Evaluate side-chains 354 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 323 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 11 LYS Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 188 GLN Chi-restraints excluded: chain M residue 343 LYS Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 0.9980 chunk 40 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN B 80 GLN B 212 ASN B 319 GLN B 505 GLN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.131286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115706 restraints weight = 18177.177| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.96 r_work: 0.3473 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13951 Z= 0.109 Angle : 0.491 10.245 18886 Z= 0.256 Chirality : 0.040 0.224 2198 Planarity : 0.004 0.050 2403 Dihedral : 4.272 49.655 1871 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 2.88 % Allowed : 25.69 % Favored : 71.43 % 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 are not related in a simple way. whole: 1.77 (0.21), residues: 1703 helix: 2.09 (0.16), residues: 1020 sheet: 1.26 (0.37), residues: 184 loop : -0.82 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 166 TYR 0.013 0.001 TYR B 72 PHE 0.012 0.001 PHE M 93 TRP 0.015 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00249 (13951) covalent geometry : angle 0.49094 (18886) hydrogen bonds : bond 0.03680 ( 817) hydrogen bonds : angle 3.94719 ( 2376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.565 Fit side-chains REVERT: A 10 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.4694 (mpp) REVERT: A 323 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: B 82 ASP cc_start: 0.7839 (m-30) cc_final: 0.7609 (m-30) REVERT: B 167 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: B 186 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7672 (tt0) REVERT: B 200 ASN cc_start: 0.5378 (m-40) cc_final: 0.4992 (p0) REVERT: B 208 LEU cc_start: 0.8704 (mt) cc_final: 0.8501 (mp) REVERT: M 1 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7803 (mpp) REVERT: M 310 ASN cc_start: 0.8274 (m110) cc_final: 0.8059 (m110) REVERT: M 408 GLU cc_start: 0.7616 (tp30) cc_final: 0.7040 (tp30) REVERT: M 432 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7911 (mt-10) REVERT: S 111 TYR cc_start: 0.8613 (m-80) cc_final: 0.8302 (m-80) REVERT: S 132 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8304 (mt) REVERT: S 137 MET cc_start: 0.8167 (tmm) cc_final: 0.7882 (tmm) outliers start: 44 outliers final: 26 residues processed: 351 average time/residue: 0.8095 time to fit residues: 303.9160 Evaluate side-chains 355 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 11 LYS Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 169 ARG Chi-restraints excluded: chain M residue 423 ARG Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 132 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 28 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 212 ASN B 505 GLN B 512 GLN M 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114362 restraints weight = 18080.942| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.93 r_work: 0.3456 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13951 Z= 0.139 Angle : 0.529 12.552 18886 Z= 0.273 Chirality : 0.041 0.232 2198 Planarity : 0.004 0.050 2403 Dihedral : 4.306 49.182 1871 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 3.01 % Allowed : 25.95 % Favored : 71.04 % 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: 1.68 (0.20), residues: 1703 helix: 2.04 (0.16), residues: 1020 sheet: 1.20 (0.37), residues: 185 loop : -0.89 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 166 TYR 0.015 0.001 TYR B 276 PHE 0.017 0.001 PHE M 56 TRP 0.011 0.001 TRP A 462 HIS 0.008 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00335 (13951) covalent geometry : angle 0.52855 (18886) hydrogen bonds : bond 0.04137 ( 817) hydrogen bonds : angle 4.01437 ( 2376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 330 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 10 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.4714 (mpp) REVERT: A 323 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: B 82 ASP cc_start: 0.7859 (m-30) cc_final: 0.7646 (m-30) REVERT: B 167 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: B 169 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7273 (tt) REVERT: B 186 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7691 (tt0) REVERT: B 200 ASN cc_start: 0.5394 (m-40) cc_final: 0.5002 (p0) REVERT: B 208 LEU cc_start: 0.8709 (mt) cc_final: 0.8501 (mp) REVERT: M 1 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7925 (mpp) REVERT: M 80 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7719 (mm-30) REVERT: M 129 LEU cc_start: 0.8023 (mt) cc_final: 0.7634 (mp) REVERT: M 188 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7660 (mm-40) REVERT: M 310 ASN cc_start: 0.8264 (m110) cc_final: 0.8054 (m110) REVERT: M 328 LEU cc_start: 0.8544 (mp) cc_final: 0.8315 (mt) REVERT: M 408 GLU cc_start: 0.7655 (tp30) cc_final: 0.7114 (tp30) REVERT: M 432 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7938 (mt-10) REVERT: S 111 TYR cc_start: 0.8640 (m-80) cc_final: 0.8332 (m-80) outliers start: 46 outliers final: 25 residues processed: 355 average time/residue: 0.8183 time to fit residues: 310.6940 Evaluate side-chains 355 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 11 LYS Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain M residue 188 GLN Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 505 GLN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115092 restraints weight = 18202.220| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3465 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13951 Z= 0.119 Angle : 0.512 12.621 18886 Z= 0.266 Chirality : 0.040 0.231 2198 Planarity : 0.004 0.049 2403 Dihedral : 4.287 50.408 1871 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.30 % Rotamer: Outliers : 2.10 % Allowed : 26.80 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.21), residues: 1703 helix: 2.09 (0.16), residues: 1019 sheet: 1.27 (0.37), residues: 183 loop : -0.88 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 166 TYR 0.014 0.001 TYR B 276 PHE 0.014 0.001 PHE M 56 TRP 0.015 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00277 (13951) covalent geometry : angle 0.51228 (18886) hydrogen bonds : bond 0.03874 ( 817) hydrogen bonds : angle 3.97886 ( 2376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 321 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 10 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.4610 (mpp) REVERT: A 323 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: B 82 ASP cc_start: 0.7796 (m-30) cc_final: 0.7581 (m-30) REVERT: B 167 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: B 169 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7288 (tt) REVERT: B 186 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7715 (tt0) REVERT: B 200 ASN cc_start: 0.5428 (m-40) cc_final: 0.5034 (p0) REVERT: B 342 MET cc_start: 0.8576 (mtm) cc_final: 0.8374 (ttp) REVERT: M 1 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7980 (mpp) REVERT: M 129 LEU cc_start: 0.8057 (mt) cc_final: 0.7655 (mp) REVERT: M 310 ASN cc_start: 0.8262 (m110) cc_final: 0.8052 (m110) REVERT: S 132 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8317 (mt) REVERT: S 137 MET cc_start: 0.8190 (tmm) cc_final: 0.7880 (tmm) outliers start: 32 outliers final: 23 residues processed: 340 average time/residue: 0.8111 time to fit residues: 295.0315 Evaluate side-chains 354 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 325 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 11 LYS Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 72 optimal weight: 0.0470 chunk 127 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS B 212 ASN B 505 GLN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117296 restraints weight = 18027.747| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.94 r_work: 0.3497 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13951 Z= 0.099 Angle : 0.503 12.649 18886 Z= 0.259 Chirality : 0.040 0.228 2198 Planarity : 0.004 0.048 2403 Dihedral : 4.189 52.851 1871 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.76 % Favored : 96.07 % Rotamer: Outliers : 1.44 % Allowed : 27.72 % Favored : 70.84 % 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: 1.83 (0.21), residues: 1703 helix: 2.16 (0.16), residues: 1019 sheet: 1.12 (0.37), residues: 185 loop : -0.77 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 166 TYR 0.012 0.001 TYR B 72 PHE 0.012 0.001 PHE A 484 TRP 0.022 0.001 TRP A 462 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00214 (13951) covalent geometry : angle 0.50326 (18886) hydrogen bonds : bond 0.03220 ( 817) hydrogen bonds : angle 3.84340 ( 2376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 328 time to evaluate : 0.602 Fit side-chains REVERT: A 10 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.4643 (mpp) REVERT: A 323 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: B 82 ASP cc_start: 0.7758 (m-30) cc_final: 0.7527 (m-30) REVERT: B 114 ARG cc_start: 0.6766 (tpm170) cc_final: 0.5804 (tmt90) REVERT: B 167 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: B 169 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7212 (tt) REVERT: B 186 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7682 (tt0) REVERT: B 200 ASN cc_start: 0.5387 (m-40) cc_final: 0.5050 (p0) REVERT: B 342 MET cc_start: 0.8495 (mtm) cc_final: 0.8284 (ttp) REVERT: M 1 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7894 (mpp) REVERT: M 80 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7832 (mm-30) REVERT: M 129 LEU cc_start: 0.8028 (mt) cc_final: 0.7633 (mp) REVERT: M 310 ASN cc_start: 0.8274 (m110) cc_final: 0.8065 (m110) REVERT: M 361 MET cc_start: 0.8607 (mmm) cc_final: 0.8239 (mmt) REVERT: M 408 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7104 (tm-30) REVERT: M 432 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7847 (mt-10) REVERT: S 132 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8311 (mt) REVERT: S 137 MET cc_start: 0.8150 (tmm) cc_final: 0.7835 (tmm) outliers start: 22 outliers final: 14 residues processed: 339 average time/residue: 0.8301 time to fit residues: 300.6963 Evaluate side-chains 334 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 314 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 68 optimal weight: 0.0570 chunk 140 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 505 GLN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116035 restraints weight = 18112.864| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.93 r_work: 0.3481 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13951 Z= 0.114 Angle : 0.516 12.189 18886 Z= 0.266 Chirality : 0.040 0.226 2198 Planarity : 0.004 0.049 2403 Dihedral : 4.199 52.734 1871 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 1.77 % Allowed : 27.59 % Favored : 70.64 % 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: 1.84 (0.21), residues: 1703 helix: 2.15 (0.16), residues: 1019 sheet: 1.25 (0.38), residues: 185 loop : -0.78 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 166 TYR 0.013 0.001 TYR B 276 PHE 0.013 0.001 PHE A 484 TRP 0.014 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00264 (13951) covalent geometry : angle 0.51570 (18886) hydrogen bonds : bond 0.03608 ( 817) hydrogen bonds : angle 3.88459 ( 2376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6544.50 seconds wall clock time: 111 minutes 52.91 seconds (6712.91 seconds total)