Starting phenix.real_space_refine on Thu Mar 14 18:37:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3e_22020/03_2024/6x3e_22020.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3e_22020/03_2024/6x3e_22020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3e_22020/03_2024/6x3e_22020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3e_22020/03_2024/6x3e_22020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3e_22020/03_2024/6x3e_22020.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3e_22020/03_2024/6x3e_22020.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 69 5.16 5 Na 3 4.78 5 C 6200 2.51 5 N 1505 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 351": "OD1" <-> "OD2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9469 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3193 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 2 Chain: "B" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 5.18, per 1000 atoms: 0.55 Number of scatterers: 9469 At special positions: 0 Unit cell: (112.32, 108.16, 86.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 Na 3 11.00 O 1692 8.00 N 1505 7.00 C 6200 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 - 3.50 Amino acid : False - 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: 3.54 Conformation dependent library (CDL) restraints added in 1.9 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 80.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.767A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.541A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.845A pdb=" N VAL A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.611A pdb=" N TYR A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.546A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 228 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.580A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.529A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 266 removed outlier: 4.068A pdb=" N CYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.554A pdb=" N LEU A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.705A pdb=" N PHE A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 4.375A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.520A pdb=" N PHE A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.682A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.540A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.543A pdb=" N ARG A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.878A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.983A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.823A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.595A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.556A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.659A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.502A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.816A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.723A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.706A pdb=" N SER B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.641A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.584A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.551A pdb=" N GLY B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 Proline residue: B 259 - end of helix removed outlier: 3.549A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.729A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.698A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.524A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.692A pdb=" N LEU B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 4.141A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.172A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.410A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.567A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 412 through 415 removed outlier: 3.881A pdb=" N GLY B 415 " --> pdb=" O PRO B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.780A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.572A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.613A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.601A pdb=" N ALA C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.762A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 86 removed outlier: 3.657A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.747A pdb=" N SER C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.612A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.537A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.558A pdb=" N GLY C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.503A pdb=" N GLN C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.676A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 removed outlier: 3.716A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.725A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.621A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 4.243A pdb=" N ARG C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.177A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.274A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.558A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.622A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.911A pdb=" N GLY C 415 " --> pdb=" O PRO C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.777A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.591A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.598A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA5, first strand: chain 'C' and resid 164 through 167 595 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1816 1.33 - 1.45: 1998 1.45 - 1.57: 5666 1.57 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 9603 Sorted by residual: bond pdb=" N LEU C 372 " pdb=" CA LEU C 372 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.17e+00 bond pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.33e-02 5.65e+03 4.97e+00 bond pdb=" N CYS A 100 " pdb=" CA CYS A 100 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.31e-02 5.83e+03 4.78e+00 bond pdb=" N LYS A 269 " pdb=" CA LYS A 269 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.28e-02 6.10e+03 4.65e+00 bond pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.52e+00 ... (remaining 9598 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.83: 184 105.83 - 112.87: 5263 112.87 - 119.92: 3561 119.92 - 126.96: 3949 126.96 - 134.01: 70 Bond angle restraints: 13027 Sorted by residual: angle pdb=" N GLN A 122 " pdb=" CA GLN A 122 " pdb=" C GLN A 122 " ideal model delta sigma weight residual 110.44 102.53 7.91 1.20e+00 6.94e-01 4.35e+01 angle pdb=" CA LYS A 123 " pdb=" C LYS A 123 " pdb=" N VAL A 124 " ideal model delta sigma weight residual 117.17 122.37 -5.20 1.18e+00 7.18e-01 1.94e+01 angle pdb=" C VAL A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 122.40 128.71 -6.31 1.45e+00 4.76e-01 1.89e+01 angle pdb=" CA GLN A 413 " pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" C ASP C 388 " pdb=" N LEU C 389 " pdb=" CA LEU C 389 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 ... (remaining 13022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5202 17.90 - 35.79: 437 35.79 - 53.68: 84 53.68 - 71.58: 17 71.58 - 89.47: 10 Dihedral angle restraints: 5750 sinusoidal: 2192 harmonic: 3558 Sorted by residual: dihedral pdb=" CA GLU A 272 " pdb=" C GLU A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LEU B 384 " pdb=" C LEU B 384 " pdb=" N ASN B 385 " pdb=" CA ASN B 385 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU C 384 " pdb=" C LEU C 384 " pdb=" N ASN C 385 " pdb=" CA ASN C 385 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1388 0.070 - 0.141: 237 0.141 - 0.211: 21 0.211 - 0.281: 7 0.281 - 0.352: 1 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CB VAL A 411 " pdb=" CA VAL A 411 " pdb=" CG1 VAL A 411 " pdb=" CG2 VAL A 411 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL A 426 " pdb=" CA VAL A 426 " pdb=" CG1 VAL A 426 " pdb=" CG2 VAL A 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1651 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO B 302 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO C 302 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.042 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO A 302 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.035 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 82 2.65 - 3.21: 8339 3.21 - 3.77: 14585 3.77 - 4.34: 20502 4.34 - 4.90: 33380 Nonbonded interactions: 76888 Sorted by model distance: nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.083 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.228 2.470 nonbonded pdb=" O ASN A 366 " pdb="NA NA A 601 " model vdw 2.293 2.470 nonbonded pdb=" O PRO B 69 " pdb=" OG SER B 73 " model vdw 2.301 2.440 nonbonded pdb=" O ALA A 456 " pdb=" OG1 THR A 459 " model vdw 2.317 2.440 ... (remaining 76883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 121 or resid 137 through 474)) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.010 Extract box with map and model: 5.590 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.580 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.006 0.063 9603 Z= 0.346 Angle : 0.904 8.675 13027 Z= 0.500 Chirality : 0.055 0.352 1654 Planarity : 0.007 0.070 1585 Dihedral : 14.423 89.473 3454 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.06 (0.15), residues: 1223 helix: -4.16 (0.08), residues: 954 sheet: -2.40 (0.81), residues: 54 loop : -1.89 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 276 HIS 0.003 0.001 HIS C 41 PHE 0.022 0.003 PHE B 159 TYR 0.024 0.002 TYR C 373 ARG 0.003 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9037 (mp) cc_final: 0.8808 (tp) REVERT: A 112 LEU cc_start: 0.8818 (mt) cc_final: 0.8537 (mt) REVERT: A 277 GLU cc_start: 0.8270 (tp30) cc_final: 0.7885 (tp30) REVERT: B 19 TRP cc_start: 0.7039 (t60) cc_final: 0.5389 (m100) REVERT: B 93 ARG cc_start: 0.8504 (mtt180) cc_final: 0.7722 (mtt180) REVERT: B 140 ASP cc_start: 0.7915 (m-30) cc_final: 0.7557 (m-30) REVERT: B 228 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7889 (mmmt) REVERT: B 280 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7459 (tpt170) REVERT: B 354 ILE cc_start: 0.8661 (mt) cc_final: 0.8310 (mm) REVERT: B 444 ASP cc_start: 0.8898 (t0) cc_final: 0.8466 (t0) REVERT: B 465 LEU cc_start: 0.8761 (mt) cc_final: 0.8457 (mt) REVERT: C 97 TYR cc_start: 0.9153 (t80) cc_final: 0.8689 (t80) REVERT: C 397 ILE cc_start: 0.9506 (mm) cc_final: 0.9256 (mm) REVERT: C 446 PHE cc_start: 0.8519 (m-80) cc_final: 0.8242 (m-80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2156 time to fit residues: 87.9892 Evaluate side-chains 198 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9603 Z= 0.148 Angle : 0.591 7.950 13027 Z= 0.300 Chirality : 0.039 0.146 1654 Planarity : 0.005 0.038 1585 Dihedral : 4.565 17.939 1302 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.40 % Allowed : 15.92 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.20), residues: 1223 helix: -1.77 (0.14), residues: 948 sheet: -2.13 (0.77), residues: 54 loop : -2.19 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 441 HIS 0.001 0.000 HIS A 41 PHE 0.019 0.002 PHE C 306 TYR 0.010 0.001 TYR A 97 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8902 (mp) cc_final: 0.8633 (tp) REVERT: A 40 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 112 LEU cc_start: 0.8528 (mt) cc_final: 0.8262 (mt) REVERT: A 277 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: A 463 GLU cc_start: 0.8257 (tt0) cc_final: 0.7705 (tm-30) REVERT: B 19 TRP cc_start: 0.6898 (t60) cc_final: 0.5392 (m100) REVERT: B 220 LEU cc_start: 0.8992 (tt) cc_final: 0.8068 (mt) REVERT: B 280 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7567 (tpt170) REVERT: B 354 ILE cc_start: 0.8627 (mt) cc_final: 0.8343 (mm) REVERT: B 368 ASP cc_start: 0.9135 (m-30) cc_final: 0.8749 (m-30) REVERT: C 97 TYR cc_start: 0.8892 (t80) cc_final: 0.8546 (t80) REVERT: C 206 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7363 (t80) REVERT: C 441 TRP cc_start: 0.8341 (p-90) cc_final: 0.8097 (p-90) outliers start: 25 outliers final: 13 residues processed: 232 average time/residue: 0.1889 time to fit residues: 62.9063 Evaluate side-chains 188 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN C 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9603 Z= 0.184 Angle : 0.568 9.124 13027 Z= 0.284 Chirality : 0.039 0.141 1654 Planarity : 0.004 0.028 1585 Dihedral : 4.190 17.718 1302 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.78 % Allowed : 18.70 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1223 helix: -0.46 (0.16), residues: 952 sheet: -1.81 (0.77), residues: 54 loop : -2.00 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 441 HIS 0.002 0.000 HIS A 296 PHE 0.019 0.002 PHE B 357 TYR 0.011 0.001 TYR B 98 ARG 0.004 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8488 (mt) cc_final: 0.8215 (mt) REVERT: A 277 GLU cc_start: 0.8297 (tp30) cc_final: 0.7288 (tp30) REVERT: A 463 GLU cc_start: 0.8235 (tt0) cc_final: 0.7826 (tm-30) REVERT: B 19 TRP cc_start: 0.7023 (t60) cc_final: 0.5402 (m100) REVERT: B 280 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7559 (tpt170) REVERT: B 354 ILE cc_start: 0.8644 (mt) cc_final: 0.8370 (mm) REVERT: B 368 ASP cc_start: 0.9218 (m-30) cc_final: 0.8844 (m-30) REVERT: C 97 TYR cc_start: 0.8826 (t80) cc_final: 0.8497 (t80) REVERT: C 206 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 441 TRP cc_start: 0.8436 (p-90) cc_final: 0.8209 (p-90) outliers start: 29 outliers final: 16 residues processed: 203 average time/residue: 0.1871 time to fit residues: 54.7115 Evaluate side-chains 187 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9603 Z= 0.148 Angle : 0.528 9.624 13027 Z= 0.264 Chirality : 0.038 0.142 1654 Planarity : 0.003 0.027 1585 Dihedral : 4.006 17.278 1302 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.55 % Allowed : 19.56 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1223 helix: 0.21 (0.17), residues: 953 sheet: -1.50 (0.77), residues: 54 loop : -1.91 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 441 HIS 0.001 0.000 HIS B 41 PHE 0.022 0.001 PHE A 306 TYR 0.017 0.001 TYR C 98 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 TRP cc_start: 0.7138 (t60) cc_final: 0.5423 (m100) REVERT: B 220 LEU cc_start: 0.8963 (tt) cc_final: 0.8030 (mt) REVERT: B 280 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7596 (tpt170) REVERT: B 354 ILE cc_start: 0.8613 (mt) cc_final: 0.8357 (mm) REVERT: B 368 ASP cc_start: 0.9165 (m-30) cc_final: 0.8785 (m-30) REVERT: B 447 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8042 (mtm-85) REVERT: B 449 MET cc_start: 0.7852 (tmm) cc_final: 0.7555 (tmm) REVERT: C 206 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7403 (t80) outliers start: 37 outliers final: 28 residues processed: 203 average time/residue: 0.1793 time to fit residues: 53.0405 Evaluate side-chains 196 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9603 Z= 0.141 Angle : 0.522 10.547 13027 Z= 0.258 Chirality : 0.038 0.124 1654 Planarity : 0.003 0.031 1585 Dihedral : 3.883 17.528 1302 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.55 % Allowed : 20.23 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1223 helix: 0.62 (0.18), residues: 955 sheet: -1.35 (0.78), residues: 54 loop : -1.84 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 441 HIS 0.001 0.000 HIS A 296 PHE 0.023 0.001 PHE B 357 TYR 0.018 0.001 TYR C 98 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 1.144 Fit side-chains REVERT: A 40 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 202 ILE cc_start: 0.8429 (mm) cc_final: 0.8218 (mm) REVERT: A 280 ARG cc_start: 0.5846 (mtt180) cc_final: 0.4890 (tpt-90) REVERT: B 19 TRP cc_start: 0.7149 (t60) cc_final: 0.5399 (m100) REVERT: B 220 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 280 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7602 (tpt170) REVERT: B 354 ILE cc_start: 0.8588 (mt) cc_final: 0.8324 (mm) REVERT: B 368 ASP cc_start: 0.9123 (m-30) cc_final: 0.8740 (m-30) REVERT: B 447 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8063 (mtm-85) REVERT: B 449 MET cc_start: 0.7809 (tmm) cc_final: 0.7491 (tmm) REVERT: B 467 LYS cc_start: 0.8091 (ptmt) cc_final: 0.7572 (pttm) REVERT: C 60 MET cc_start: 0.8505 (mmm) cc_final: 0.8209 (mmp) REVERT: C 206 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7355 (t80) outliers start: 37 outliers final: 25 residues processed: 205 average time/residue: 0.1882 time to fit residues: 55.7599 Evaluate side-chains 198 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9603 Z= 0.254 Angle : 0.579 10.775 13027 Z= 0.288 Chirality : 0.041 0.137 1654 Planarity : 0.003 0.030 1585 Dihedral : 4.048 18.330 1302 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.84 % Allowed : 20.33 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1223 helix: 0.69 (0.18), residues: 950 sheet: -1.28 (0.77), residues: 54 loop : -1.74 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 441 HIS 0.006 0.001 HIS A 296 PHE 0.019 0.002 PHE A 240 TYR 0.028 0.002 TYR C 98 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.139 Fit side-chains REVERT: A 280 ARG cc_start: 0.5823 (mtt180) cc_final: 0.4793 (tpt-90) REVERT: B 19 TRP cc_start: 0.7147 (t60) cc_final: 0.5404 (m100) REVERT: B 220 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8031 (mt) REVERT: B 280 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7653 (tpt170) REVERT: B 354 ILE cc_start: 0.8629 (mt) cc_final: 0.8371 (mm) REVERT: B 467 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7629 (pttm) REVERT: C 206 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7193 (t80) REVERT: C 312 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8025 (t0) REVERT: C 441 TRP cc_start: 0.8446 (p-90) cc_final: 0.8238 (p-90) outliers start: 40 outliers final: 29 residues processed: 194 average time/residue: 0.1815 time to fit residues: 51.0495 Evaluate side-chains 190 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9603 Z= 0.145 Angle : 0.523 8.983 13027 Z= 0.259 Chirality : 0.038 0.121 1654 Planarity : 0.003 0.033 1585 Dihedral : 3.881 19.118 1302 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.26 % Allowed : 21.00 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1223 helix: 1.01 (0.18), residues: 951 sheet: -1.28 (0.76), residues: 54 loop : -1.74 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 441 HIS 0.004 0.001 HIS A 296 PHE 0.026 0.001 PHE B 357 TYR 0.027 0.001 TYR C 98 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.164 Fit side-chains REVERT: A 280 ARG cc_start: 0.5965 (mtt180) cc_final: 0.4859 (tpt-90) REVERT: A 455 ASP cc_start: 0.7682 (m-30) cc_final: 0.7474 (m-30) REVERT: B 19 TRP cc_start: 0.7141 (t60) cc_final: 0.5363 (m100) REVERT: B 220 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.7912 (mt) REVERT: B 280 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7638 (tpt170) REVERT: B 368 ASP cc_start: 0.9175 (m-30) cc_final: 0.8833 (m-30) REVERT: B 449 MET cc_start: 0.7810 (tmm) cc_final: 0.7487 (tmm) REVERT: B 467 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7636 (pttm) REVERT: C 60 MET cc_start: 0.8551 (mmm) cc_final: 0.8247 (mmp) REVERT: C 206 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7270 (t80) REVERT: C 312 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7918 (t0) REVERT: C 441 TRP cc_start: 0.8410 (p-90) cc_final: 0.8179 (p-90) outliers start: 34 outliers final: 21 residues processed: 200 average time/residue: 0.1808 time to fit residues: 52.9391 Evaluate side-chains 184 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.0670 chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9603 Z= 0.197 Angle : 0.558 8.225 13027 Z= 0.275 Chirality : 0.040 0.123 1654 Planarity : 0.003 0.033 1585 Dihedral : 3.897 17.290 1302 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.88 % Allowed : 21.76 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1223 helix: 1.03 (0.18), residues: 953 sheet: -1.11 (0.77), residues: 54 loop : -1.60 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.021 0.002 PHE C 357 TYR 0.029 0.001 TYR C 98 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.052 Fit side-chains REVERT: A 40 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: A 280 ARG cc_start: 0.6020 (mtt180) cc_final: 0.4915 (tpt-90) REVERT: B 19 TRP cc_start: 0.7117 (t60) cc_final: 0.5371 (m100) REVERT: B 220 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.7888 (mt) REVERT: B 280 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7637 (tpt170) REVERT: B 449 MET cc_start: 0.7824 (tmm) cc_final: 0.7512 (tmm) REVERT: B 467 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7655 (pttm) REVERT: C 206 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7226 (t80) REVERT: C 312 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7973 (t0) REVERT: C 441 TRP cc_start: 0.8402 (p-90) cc_final: 0.8147 (p-90) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.1820 time to fit residues: 48.6543 Evaluate side-chains 183 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9603 Z= 0.152 Angle : 0.539 8.492 13027 Z= 0.264 Chirality : 0.039 0.121 1654 Planarity : 0.003 0.034 1585 Dihedral : 3.834 16.722 1302 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.59 % Allowed : 22.44 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1223 helix: 1.23 (0.18), residues: 943 sheet: -1.09 (0.76), residues: 54 loop : -1.69 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.022 0.001 PHE C 357 TYR 0.029 0.002 TYR C 98 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.140 Fit side-chains REVERT: A 280 ARG cc_start: 0.6013 (mtt180) cc_final: 0.4920 (tpt-90) REVERT: B 19 TRP cc_start: 0.7157 (t60) cc_final: 0.5366 (m100) REVERT: B 220 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.7909 (mt) REVERT: B 280 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7646 (tpt170) REVERT: B 449 MET cc_start: 0.7806 (tmm) cc_final: 0.7476 (tmm) REVERT: C 206 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7246 (t80) REVERT: C 312 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7970 (t0) REVERT: C 441 TRP cc_start: 0.8404 (p-90) cc_final: 0.8143 (p-90) outliers start: 27 outliers final: 22 residues processed: 185 average time/residue: 0.1720 time to fit residues: 46.8508 Evaluate side-chains 184 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9603 Z= 0.192 Angle : 0.559 8.606 13027 Z= 0.276 Chirality : 0.039 0.124 1654 Planarity : 0.003 0.034 1585 Dihedral : 3.896 16.871 1302 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.78 % Allowed : 22.53 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1223 helix: 1.23 (0.18), residues: 943 sheet: -1.06 (0.76), residues: 54 loop : -1.57 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.025 0.001 PHE C 357 TYR 0.030 0.001 TYR C 98 ARG 0.006 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.068 Fit side-chains REVERT: A 280 ARG cc_start: 0.6005 (mtt180) cc_final: 0.4913 (tpt-90) REVERT: B 19 TRP cc_start: 0.7124 (t60) cc_final: 0.5363 (m100) REVERT: B 220 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.7882 (mt) REVERT: B 280 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7661 (tpt170) REVERT: B 449 MET cc_start: 0.7830 (tmm) cc_final: 0.7514 (tmm) REVERT: B 467 LYS cc_start: 0.8141 (ptmt) cc_final: 0.7770 (pttm) REVERT: C 206 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7208 (t80) REVERT: C 312 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8063 (t0) REVERT: C 441 TRP cc_start: 0.8386 (p-90) cc_final: 0.8105 (p-90) outliers start: 29 outliers final: 24 residues processed: 182 average time/residue: 0.1899 time to fit residues: 51.0834 Evaluate side-chains 186 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099242 restraints weight = 15188.992| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.24 r_work: 0.2923 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9603 Z= 0.152 Angle : 0.539 8.467 13027 Z= 0.265 Chirality : 0.039 0.121 1654 Planarity : 0.003 0.034 1585 Dihedral : 3.835 15.889 1302 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.59 % Allowed : 22.44 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1223 helix: 1.32 (0.18), residues: 949 sheet: -1.06 (0.76), residues: 54 loop : -1.55 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 441 HIS 0.004 0.001 HIS A 296 PHE 0.021 0.001 PHE A 306 TYR 0.029 0.001 TYR C 98 ARG 0.006 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.06 seconds wall clock time: 39 minutes 17.71 seconds (2357.71 seconds total)