Starting phenix.real_space_refine on Sat Aug 3 08:22:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6n_37329/08_2024/8w6n_37329.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6n_37329/08_2024/8w6n_37329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6n_37329/08_2024/8w6n_37329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6n_37329/08_2024/8w6n_37329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6n_37329/08_2024/8w6n_37329.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6n_37329/08_2024/8w6n_37329.cif" } resolution = 3.2 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= 0.111 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 55 5.16 5 Na 1 4.78 5 C 5110 2.51 5 N 1158 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 277": "NH1" <-> "NH2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3857 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 30, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3748 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 30, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.94, per 1000 atoms: 0.65 Number of scatterers: 7616 At special positions: 0 Unit cell: (91.308, 92.395, 105.439, 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 55 16.00 Na 1 11.00 O 1292 8.00 N 1158 7.00 C 5110 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 65.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 4.145A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.611A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.581A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.865A pdb=" N TRP A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 50' Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.516A pdb=" N LEU A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.701A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.728A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.520A pdb=" N MET A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.612A pdb=" N SER A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 146 through 161 removed outlier: 4.230A pdb=" N ILE A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 4.146A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.538A pdb=" N ASN A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.681A pdb=" N SER A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.837A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 339 removed outlier: 4.000A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.817A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.886A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.661A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.574A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.627A pdb=" N ILE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix removed outlier: 3.934A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.808A pdb=" N TYR A 542 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 543' Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.642A pdb=" N ALA A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.054A pdb=" N VAL B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.544A pdb=" N THR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.820A pdb=" N PHE B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 79 through 82 removed outlier: 3.951A pdb=" N PHE B 82 " --> pdb=" O SER B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.590A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 removed outlier: 3.622A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.501A pdb=" N GLY B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N MET B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.549A pdb=" N VAL B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.542A pdb=" N GLU B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.693A pdb=" N LYS B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 245 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.610A pdb=" N GLY B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.800A pdb=" N LEU B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.632A pdb=" N PHE B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 removed outlier: 3.559A pdb=" N LEU B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.545A pdb=" N ALA B 330 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 4.098A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.914A pdb=" N ALA B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.590A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.601A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.619A pdb=" N ILE B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.670A pdb=" N SER B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Proline residue: B 503 - end of helix removed outlier: 3.612A pdb=" N ALA B 507 " --> pdb=" O PRO B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.926A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.611A pdb=" N LEU B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 522 " --> pdb=" O PRO B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 534 through 539 removed outlier: 4.296A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.561A pdb=" N VAL B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.735A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.809A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 735 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: 1.87 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2166 1.34 - 1.46: 1872 1.46 - 1.58: 3712 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 7836 Sorted by residual: bond pdb=" N THR A 423 " pdb=" CA THR A 423 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.01e+00 bond pdb=" O3 SO4 B 701 " pdb=" S SO4 B 701 " ideal model delta sigma weight residual 1.499 1.457 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" O4 SO4 B 701 " pdb=" S SO4 B 701 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" O3 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" O1 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.498 1.458 0.040 2.00e-02 2.50e+03 3.95e+00 ... (remaining 7831 not shown) Histogram of bond angle deviations from ideal: 100.10 - 107.46: 402 107.46 - 114.82: 4641 114.82 - 122.18: 4427 122.18 - 129.54: 1147 129.54 - 136.90: 104 Bond angle restraints: 10721 Sorted by residual: angle pdb=" N ILE A 538 " pdb=" CA ILE A 538 " pdb=" C ILE A 538 " ideal model delta sigma weight residual 111.91 105.26 6.65 8.90e-01 1.26e+00 5.58e+01 angle pdb=" C ILE B 573 " pdb=" N VAL B 574 " pdb=" CA VAL B 574 " ideal model delta sigma weight residual 120.24 124.07 -3.83 6.30e-01 2.52e+00 3.70e+01 angle pdb=" CA LEU B 545 " pdb=" CB LEU B 545 " pdb=" CG LEU B 545 " ideal model delta sigma weight residual 116.30 136.90 -20.60 3.50e+00 8.16e-02 3.46e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.67 106.60 5.07 9.50e-01 1.11e+00 2.85e+01 angle pdb=" C VAL B 113 " pdb=" N MET B 114 " pdb=" CA MET B 114 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 ... (remaining 10716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4097 17.68 - 35.36: 381 35.36 - 53.04: 50 53.04 - 70.72: 5 70.72 - 88.40: 2 Dihedral angle restraints: 4535 sinusoidal: 1697 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG B 364 " pdb=" C ARG B 364 " pdb=" N ASP B 365 " pdb=" CA ASP B 365 " ideal model delta harmonic sigma weight residual 180.00 147.58 32.42 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA TYR B 582 " pdb=" C TYR B 582 " pdb=" N PRO B 583 " pdb=" CA PRO B 583 " ideal model delta harmonic sigma weight residual 180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU B 529 " pdb=" C LEU B 529 " pdb=" N PRO B 530 " pdb=" CA PRO B 530 " ideal model delta harmonic sigma weight residual -180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 921 0.050 - 0.101: 286 0.101 - 0.151: 62 0.151 - 0.202: 18 0.202 - 0.252: 4 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 538 " pdb=" CA ILE A 538 " pdb=" CG1 ILE A 538 " pdb=" CG2 ILE A 538 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1288 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 535 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " 0.053 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO A 25 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " 0.053 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO A 535 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.044 5.00e-02 4.00e+02 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2493 2.83 - 3.35: 6502 3.35 - 3.86: 11967 3.86 - 4.38: 14678 4.38 - 4.90: 24704 Nonbonded interactions: 60344 Sorted by model distance: nonbonded pdb=" O ILE A 93 " pdb=" OG1 THR A 97 " model vdw 2.310 3.040 nonbonded pdb=" O LEU B 498 " pdb=" OG SER B 502 " model vdw 2.312 3.040 nonbonded pdb=" O SER A 139 " pdb=" OG1 THR A 143 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR B 141 " pdb=" O3 SO4 B 701 " model vdw 2.323 3.040 nonbonded pdb=" O ALA B 59 " pdb=" OH TYR B 81 " model vdw 2.326 3.040 ... (remaining 60339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 161 or resid 233 through 309 or resid 325 throug \ h 403 or resid 418 through 588)) selection = (chain 'B' and resid 8 through 588) } 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: 0.820 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.370 Find NCS groups from input model: 0.300 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7836 Z= 0.277 Angle : 0.952 20.596 10721 Z= 0.511 Chirality : 0.053 0.252 1291 Planarity : 0.010 0.104 1274 Dihedral : 13.428 88.400 2693 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -7.03 (0.15), residues: 959 helix: -4.80 (0.06), residues: 635 sheet: None (None), residues: 0 loop : -3.88 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 424 HIS 0.004 0.001 HIS B 105 PHE 0.020 0.001 PHE A 540 TYR 0.024 0.001 TYR A 514 ARG 0.001 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 0.858 Fit side-chains REVERT: A 128 MET cc_start: 0.8936 (mtp) cc_final: 0.8664 (mtp) REVERT: A 338 GLN cc_start: 0.8248 (mm110) cc_final: 0.7952 (mm110) REVERT: A 480 MET cc_start: 0.8261 (ttm) cc_final: 0.8028 (ttm) REVERT: A 546 LYS cc_start: 0.8066 (mttt) cc_final: 0.7744 (mmtt) REVERT: B 430 PHE cc_start: 0.7864 (t80) cc_final: 0.7586 (t80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1864 time to fit residues: 45.7368 Evaluate side-chains 133 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 39 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 428 GLN B 86 HIS B 103 ASN B 160 ASN B 270 ASN B 325 GLN B 338 GLN B 346 GLN B 490 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7836 Z= 0.170 Angle : 0.660 12.766 10721 Z= 0.333 Chirality : 0.042 0.153 1291 Planarity : 0.007 0.078 1274 Dihedral : 5.596 29.707 1012 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.63 % Allowed : 11.00 % Favored : 86.36 % 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: -4.98 (0.21), residues: 959 helix: -3.15 (0.14), residues: 635 sheet: None (None), residues: 0 loop : -3.23 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 572 HIS 0.002 0.001 HIS B 86 PHE 0.015 0.001 PHE A 368 TYR 0.020 0.001 TYR A 514 ARG 0.006 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.832 Fit side-chains REVERT: A 128 MET cc_start: 0.8928 (mtp) cc_final: 0.8603 (mtp) REVERT: A 338 GLN cc_start: 0.8373 (mm110) cc_final: 0.8160 (mm110) REVERT: A 480 MET cc_start: 0.8096 (ttm) cc_final: 0.7756 (ttp) REVERT: B 430 PHE cc_start: 0.7877 (t80) cc_final: 0.7666 (t80) outliers start: 22 outliers final: 11 residues processed: 162 average time/residue: 0.1780 time to fit residues: 39.8383 Evaluate side-chains 141 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 343 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7836 Z= 0.195 Angle : 0.646 11.488 10721 Z= 0.319 Chirality : 0.043 0.150 1291 Planarity : 0.006 0.071 1274 Dihedral : 5.321 27.580 1012 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.71 % Allowed : 14.00 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.82 (0.24), residues: 959 helix: -2.18 (0.18), residues: 643 sheet: None (None), residues: 0 loop : -3.00 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 572 HIS 0.002 0.001 HIS B 31 PHE 0.013 0.001 PHE A 368 TYR 0.017 0.001 TYR A 514 ARG 0.004 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8952 (mtp) cc_final: 0.8640 (mtp) REVERT: B 430 PHE cc_start: 0.7887 (t80) cc_final: 0.7669 (t80) REVERT: B 480 MET cc_start: 0.7618 (ttm) cc_final: 0.7241 (ttp) outliers start: 31 outliers final: 19 residues processed: 162 average time/residue: 0.1805 time to fit residues: 40.2871 Evaluate side-chains 154 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 157 GLN B 234 HIS ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7836 Z= 0.169 Angle : 0.614 10.553 10721 Z= 0.302 Chirality : 0.042 0.143 1291 Planarity : 0.006 0.066 1274 Dihedral : 5.062 26.448 1012 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.35 % Allowed : 15.67 % Favored : 80.98 % 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: -3.03 (0.26), residues: 959 helix: -1.57 (0.20), residues: 641 sheet: None (None), residues: 0 loop : -2.70 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 572 HIS 0.002 0.000 HIS B 86 PHE 0.013 0.001 PHE A 368 TYR 0.016 0.001 TYR A 514 ARG 0.003 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8990 (mtp) cc_final: 0.8696 (mtp) REVERT: A 480 MET cc_start: 0.8100 (ttm) cc_final: 0.7824 (ttp) REVERT: B 368 PHE cc_start: 0.6828 (m-10) cc_final: 0.6424 (m-80) REVERT: B 480 MET cc_start: 0.7614 (ttm) cc_final: 0.7237 (ttp) outliers start: 28 outliers final: 19 residues processed: 160 average time/residue: 0.1799 time to fit residues: 39.6167 Evaluate side-chains 153 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 428 GLN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7836 Z= 0.259 Angle : 0.652 10.169 10721 Z= 0.324 Chirality : 0.044 0.153 1291 Planarity : 0.006 0.067 1274 Dihedral : 5.237 25.938 1012 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.59 % Allowed : 16.39 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.26), residues: 959 helix: -1.38 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -2.81 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 48 HIS 0.004 0.001 HIS B 86 PHE 0.013 0.001 PHE A 368 TYR 0.016 0.001 TYR A 514 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 480 MET cc_start: 0.8184 (ttm) cc_final: 0.7969 (ttp) outliers start: 30 outliers final: 25 residues processed: 153 average time/residue: 0.1826 time to fit residues: 38.4131 Evaluate side-chains 149 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7836 Z= 0.175 Angle : 0.605 9.991 10721 Z= 0.299 Chirality : 0.042 0.145 1291 Planarity : 0.006 0.067 1274 Dihedral : 4.994 25.594 1012 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.47 % Allowed : 17.82 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.27), residues: 959 helix: -1.02 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -2.68 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 PHE 0.012 0.001 PHE A 368 TYR 0.010 0.001 TYR B 379 ARG 0.004 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 480 MET cc_start: 0.8194 (ttm) cc_final: 0.7923 (ttp) REVERT: B 480 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7318 (ttp) outliers start: 29 outliers final: 20 residues processed: 157 average time/residue: 0.1777 time to fit residues: 38.5369 Evaluate side-chains 152 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7836 Z= 0.209 Angle : 0.617 9.741 10721 Z= 0.305 Chirality : 0.043 0.145 1291 Planarity : 0.006 0.069 1274 Dihedral : 4.971 24.833 1012 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.71 % Allowed : 18.06 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.28), residues: 959 helix: -0.82 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.63 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 PHE 0.012 0.001 PHE A 368 TYR 0.014 0.001 TYR B 379 ARG 0.004 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 480 MET cc_start: 0.8176 (ttm) cc_final: 0.7952 (ttp) REVERT: B 118 VAL cc_start: 0.7363 (OUTLIER) cc_final: 0.7000 (p) REVERT: B 480 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7326 (ttp) outliers start: 31 outliers final: 26 residues processed: 155 average time/residue: 0.1759 time to fit residues: 37.5880 Evaluate side-chains 158 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 0.0000 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7836 Z= 0.170 Angle : 0.598 9.674 10721 Z= 0.295 Chirality : 0.042 0.138 1291 Planarity : 0.005 0.069 1274 Dihedral : 4.810 24.601 1012 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.47 % Allowed : 19.02 % Favored : 77.51 % 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: -1.91 (0.28), residues: 959 helix: -0.60 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.013 0.001 TYR B 379 ARG 0.003 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 480 MET cc_start: 0.8171 (ttm) cc_final: 0.7964 (ttp) REVERT: B 118 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7167 (p) REVERT: B 119 ASN cc_start: 0.6877 (OUTLIER) cc_final: 0.6512 (t0) REVERT: B 480 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7301 (ttp) outliers start: 29 outliers final: 24 residues processed: 156 average time/residue: 0.1745 time to fit residues: 37.7311 Evaluate side-chains 162 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7836 Z= 0.176 Angle : 0.607 9.594 10721 Z= 0.300 Chirality : 0.042 0.145 1291 Planarity : 0.005 0.067 1274 Dihedral : 4.779 24.138 1012 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.47 % Allowed : 19.26 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.78 (0.28), residues: 959 helix: -0.53 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.016 0.001 TYR B 379 ARG 0.004 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: B 118 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7172 (p) REVERT: B 119 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6538 (t0) REVERT: B 480 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7298 (ttp) outliers start: 29 outliers final: 22 residues processed: 158 average time/residue: 0.1829 time to fit residues: 39.9404 Evaluate side-chains 158 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 88 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7836 Z= 0.144 Angle : 0.591 9.652 10721 Z= 0.290 Chirality : 0.041 0.152 1291 Planarity : 0.005 0.066 1274 Dihedral : 4.471 24.549 1012 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.51 % Allowed : 20.22 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.57 (0.28), residues: 959 helix: -0.34 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 471 HIS 0.001 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.013 0.001 TYR B 246 ARG 0.004 0.000 ARG A 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8773 (pt) cc_final: 0.8390 (mm) REVERT: B 480 MET cc_start: 0.7552 (ttm) cc_final: 0.7232 (ttp) outliers start: 21 outliers final: 17 residues processed: 164 average time/residue: 0.1744 time to fit residues: 39.8678 Evaluate side-chains 156 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN B 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117896 restraints weight = 10423.550| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.62 r_work: 0.3098 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7836 Z= 0.179 Angle : 0.609 9.618 10721 Z= 0.301 Chirality : 0.042 0.146 1291 Planarity : 0.005 0.057 1274 Dihedral : 4.553 23.022 1012 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.39 % Allowed : 20.81 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.28), residues: 959 helix: -0.21 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -2.58 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 471 HIS 0.002 0.000 HIS B 86 PHE 0.011 0.001 PHE A 368 TYR 0.015 0.001 TYR B 580 ARG 0.004 0.000 ARG B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.60 seconds wall clock time: 35 minutes 50.88 seconds (2150.88 seconds total)