Starting phenix.real_space_refine on Mon Mar 18 11:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/03_2024/7adk_11729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/03_2024/7adk_11729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/03_2024/7adk_11729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/03_2024/7adk_11729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/03_2024/7adk_11729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/03_2024/7adk_11729.pdb" } resolution = 2.8 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= 1.000 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 9 5.16 5 C 6690 2.51 5 N 1782 2.21 5 O 2128 1.98 5 H 10260 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 397": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 473": "OD1" <-> "OD2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 624": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 636": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A ARG 715": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 611": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B GLU 690": "OE1" <-> "OE2" Residue "B ASP 731": "OD1" <-> "OD2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B ASP 792": "OD1" <-> "OD2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 847": "OD1" <-> "OD2" 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: 20869 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9710 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 22, 'TRANS': 590} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 11159 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 14, 'TRANS': 689} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 8.64, per 1000 atoms: 0.41 Number of scatterers: 20869 At special positions: 0 Unit cell: (98.77, 102.09, 132.8, 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 9 16.00 O 2128 8.00 N 1782 7.00 C 6690 6.00 H 10260 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 14.79 Conformation dependent library (CDL) restraints added in 2.4 seconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 34.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.635A pdb=" N GLU A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.529A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 removed outlier: 4.335A pdb=" N LYS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.932A pdb=" N LYS A 263 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER A 264 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.779A pdb=" N TRP A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 291 No H-bonds generated for 'chain 'A' and resid 290 through 291' Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.796A pdb=" N LYS A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.814A pdb=" N SER A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 388 removed outlier: 4.354A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.523A pdb=" N TYR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.821A pdb=" N VAL A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.610A pdb=" N GLY A 588 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.747A pdb=" N GLU A 659 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 710 removed outlier: 3.668A pdb=" N LYS A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.565A pdb=" N GLU B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 3.518A pdb=" N TYR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 219 through 227 removed outlier: 4.112A pdb=" N ALA B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.791A pdb=" N ASN B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 removed outlier: 3.846A pdb=" N ILE B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 removed outlier: 3.689A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 360 through 376 removed outlier: 4.395A pdb=" N ASP B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 366 " --> pdb=" O GLN B 362 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 413 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 520 through 524 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 639 through 643 removed outlier: 4.076A pdb=" N LYS B 642 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 removed outlier: 4.470A pdb=" N LYS B 656 " --> pdb=" O GLU B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.786A pdb=" N TYR B 673 " --> pdb=" O TYR B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.686A pdb=" N THR B 691 " --> pdb=" O LYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 720 removed outlier: 4.063A pdb=" N ASN B 720 " --> pdb=" O PHE B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 832 removed outlier: 3.782A pdb=" N LYS B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 850 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 7.351A pdb=" N GLU A 140 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL A 178 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU A 142 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 379 removed outlier: 8.627A pdb=" N SER A 448 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 417 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG A 450 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 419 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LYS A 452 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 421 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET A 454 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 516 through 517 removed outlier: 5.609A pdb=" N TYR A 517 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 554 " --> pdb=" O ASP A 610 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 609 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 641 " --> pdb=" O HIS A 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652 Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 425 removed outlier: 3.618A pdb=" N SER B 461 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 503 through 507 removed outlier: 6.550A pdb=" N ILE B 542 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS B 442 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B 446 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE B 428 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS B 836 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 535 through 537 removed outlier: 6.818A pdb=" N GLY B 535 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B 727 " --> pdb=" O TYR B 740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 594 through 595 removed outlier: 6.842A pdb=" N LYS B 594 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA B 772 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 785 " --> pdb=" O HIS B 775 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SER B 777 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR B 783 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU B 745 " --> pdb=" O ALA B 788 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 594 through 595 removed outlier: 6.842A pdb=" N LYS B 594 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA B 772 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU B 770 " --> pdb=" O THR B 765 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR B 765 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 761 " --> pdb=" O TYR B 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 790 through 792 303 hydrogen bonds defined for protein. 777 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: 7.04 Time building geometry restraints manager: 15.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 4674 1.09 - 1.27: 7446 1.27 - 1.45: 3005 1.45 - 1.64: 5938 1.64 - 1.82: 18 Bond restraints: 21081 Sorted by residual: bond pdb=" ND2 ASN A 389 " pdb="HD22 ASN A 389 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N LEU B 191 " pdb=" H LEU B 191 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NH1 ARG A 316 " pdb="HH11 ARG A 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CD2 PHE A 390 " pdb=" HD2 PHE A 390 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 TYR B 660 " pdb=" HE2 TYR B 660 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 21076 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.36: 1319 106.36 - 113.51: 22006 113.51 - 120.67: 10577 120.67 - 127.82: 3969 127.82 - 134.97: 83 Bond angle restraints: 37954 Sorted by residual: angle pdb=" CA PHE B 229 " pdb=" CB PHE B 229 " pdb=" CG PHE B 229 " ideal model delta sigma weight residual 113.80 122.61 -8.81 1.00e+00 1.00e+00 7.77e+01 angle pdb=" CA ASP B 270 " pdb=" CB ASP B 270 " pdb=" CG ASP B 270 " ideal model delta sigma weight residual 112.60 120.32 -7.72 1.00e+00 1.00e+00 5.96e+01 angle pdb=" C TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta sigma weight residual 109.95 125.18 -15.23 1.99e+00 2.53e-01 5.85e+01 angle pdb=" CA ASN B 468 " pdb=" CB ASN B 468 " pdb=" CG ASN B 468 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.66e+01 angle pdb=" CA ASP A 420 " pdb=" CB ASP A 420 " pdb=" CG ASP A 420 " ideal model delta sigma weight residual 112.60 119.91 -7.31 1.00e+00 1.00e+00 5.35e+01 ... (remaining 37949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8905 17.72 - 35.44: 732 35.44 - 53.16: 204 53.16 - 70.89: 101 70.89 - 88.61: 18 Dihedral angle restraints: 9960 sinusoidal: 5360 harmonic: 4600 Sorted by residual: dihedral pdb=" C TYR A 284 " pdb=" N TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta harmonic sigma weight residual -122.60 -142.68 20.08 0 2.50e+00 1.60e-01 6.45e+01 dihedral pdb=" CA LYS A 497 " pdb=" C LYS A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 147.49 32.51 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA SER B 421 " pdb=" C SER B 421 " pdb=" N GLU B 422 " pdb=" CA GLU B 422 " ideal model delta harmonic sigma weight residual 180.00 149.16 30.84 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 9957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1153 0.130 - 0.260: 310 0.260 - 0.390: 47 0.390 - 0.520: 11 0.520 - 0.650: 2 Chirality restraints: 1523 Sorted by residual: chirality pdb=" CA TYR A 284 " pdb=" N TYR A 284 " pdb=" C TYR A 284 " pdb=" CB TYR A 284 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE B 666 " pdb=" CA ILE B 666 " pdb=" CG1 ILE B 666 " pdb=" CG2 ILE B 666 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CG LEU B 578 " pdb=" CB LEU B 578 " pdb=" CD1 LEU B 578 " pdb=" CD2 LEU B 578 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 1520 not shown) Planarity restraints: 3193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.232 2.00e-02 2.50e+03 1.14e-01 5.19e+02 pdb=" CG TRP A 286 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " 0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.058 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " 0.116 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TRP A 286 " -0.134 2.00e-02 2.50e+03 pdb=" HE1 TRP A 286 " -0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP A 286 " -0.110 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 286 " 0.114 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 286 " -0.193 2.00e-02 2.50e+03 pdb=" HH2 TRP A 286 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 633 " 0.163 2.00e-02 2.50e+03 1.15e-01 3.99e+02 pdb=" CG TYR B 633 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 633 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 633 " -0.109 2.00e-02 2.50e+03 pdb=" CE1 TYR B 633 " -0.103 2.00e-02 2.50e+03 pdb=" CE2 TYR B 633 " -0.082 2.00e-02 2.50e+03 pdb=" CZ TYR B 633 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR B 633 " 0.244 2.00e-02 2.50e+03 pdb=" HD1 TYR B 633 " 0.078 2.00e-02 2.50e+03 pdb=" HD2 TYR B 633 " -0.100 2.00e-02 2.50e+03 pdb=" HE1 TYR B 633 " -0.147 2.00e-02 2.50e+03 pdb=" HE2 TYR B 633 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.257 2.00e-02 2.50e+03 1.10e-01 3.60e+02 pdb=" CG TYR A 284 " -0.214 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.123 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR A 284 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR A 284 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR A 284 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 TYR A 284 " 0.084 2.00e-02 2.50e+03 ... (remaining 3190 not shown) Histogram of nonbonded interaction distances: 0.12 - 1.02: 7 1.02 - 1.91: 356 1.91 - 2.81: 39596 2.81 - 3.70: 91135 3.70 - 4.60: 151618 Warning: very small nonbonded interaction distances. Nonbonded interactions: 282712 Sorted by model distance: nonbonded pdb=" CG LYS A 484 " pdb=" HZ1 LYS B 478 " model vdw 0.121 2.750 nonbonded pdb=" CD LYS A 484 " pdb=" HZ2 LYS B 478 " model vdw 0.207 2.750 nonbonded pdb=" HB3 LYS A 484 " pdb=" HE3 LYS B 478 " model vdw 0.542 2.440 nonbonded pdb=" HB3 LYS A 484 " pdb=" CE LYS B 478 " model vdw 0.970 2.920 nonbonded pdb=" HD2 LYS A 484 " pdb=" HZ2 LYS B 478 " model vdw 0.971 2.270 ... (remaining 282707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.270 Extract box with map and model: 4.670 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 61.280 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 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 : 0.014 0.118 10821 Z= 0.878 Angle : 2.029 15.226 14569 Z= 1.353 Chirality : 0.123 0.650 1523 Planarity : 0.016 0.266 1914 Dihedral : 15.241 88.607 4082 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.43 % Allowed : 7.43 % Favored : 92.13 % Cbeta Deviations : 1.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.46 (0.21), residues: 1313 helix: -3.00 (0.20), residues: 316 sheet: 0.00 (0.43), residues: 118 loop : -1.38 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.027 TRP A 286 HIS 0.016 0.006 HIS A 664 PHE 0.107 0.015 PHE B 240 TYR 0.246 0.025 TYR A 284 ARG 0.008 0.002 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8035 (mttt) REVERT: A 174 LYS cc_start: 0.7886 (tptt) cc_final: 0.7128 (ttpt) REVERT: A 222 LYS cc_start: 0.7385 (mttt) cc_final: 0.6828 (mtpt) REVERT: A 276 LYS cc_start: 0.7332 (mmmm) cc_final: 0.7035 (ttpp) REVERT: A 305 LYS cc_start: 0.6242 (pttp) cc_final: 0.6035 (mtmm) REVERT: A 391 LYS cc_start: 0.7306 (mtmm) cc_final: 0.7077 (mtmm) REVERT: A 399 SER cc_start: 0.8154 (p) cc_final: 0.7754 (m) REVERT: A 472 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6653 (ttmm) REVERT: A 475 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6729 (mm110) REVERT: A 523 ARG cc_start: 0.6912 (ttm-80) cc_final: 0.6592 (ttm-80) REVERT: A 634 GLU cc_start: 0.6893 (tt0) cc_final: 0.6320 (tm-30) REVERT: A 640 GLU cc_start: 0.7252 (tt0) cc_final: 0.6857 (mp0) REVERT: A 647 GLU cc_start: 0.6958 (mp0) cc_final: 0.6751 (mm-30) REVERT: B 165 THR cc_start: 0.7416 (t) cc_final: 0.7179 (t) REVERT: B 169 ASP cc_start: 0.7046 (m-30) cc_final: 0.6822 (m-30) REVERT: B 276 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6247 (mp0) REVERT: B 434 GLU cc_start: 0.6714 (mp0) cc_final: 0.6339 (mp0) REVERT: B 449 SER cc_start: 0.7959 (t) cc_final: 0.7410 (m) REVERT: B 507 PHE cc_start: 0.7485 (t80) cc_final: 0.7252 (t80) REVERT: B 558 TYR cc_start: 0.8202 (p90) cc_final: 0.7977 (p90) REVERT: B 642 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7918 (mtpp) REVERT: B 739 LYS cc_start: 0.6528 (mttt) cc_final: 0.6317 (mtpt) REVERT: B 828 MET cc_start: 0.7173 (ttt) cc_final: 0.6673 (mmm) REVERT: B 830 LYS cc_start: 0.7463 (pttt) cc_final: 0.7016 (pttm) outliers start: 5 outliers final: 3 residues processed: 249 average time/residue: 2.3333 time to fit residues: 630.2083 Evaluate side-chains 156 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 260 ASN A 369 ASN A 458 ASN A 461 GLN A 529 ASN A 581 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 711 ASN B 194 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10821 Z= 0.226 Angle : 0.696 8.710 14569 Z= 0.378 Chirality : 0.044 0.214 1523 Planarity : 0.004 0.060 1914 Dihedral : 7.385 40.214 1444 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.77 % Allowed : 13.83 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.94 (0.22), residues: 1313 helix: -1.90 (0.24), residues: 331 sheet: 0.56 (0.45), residues: 110 loop : -1.32 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 286 HIS 0.005 0.002 HIS B 450 PHE 0.015 0.002 PHE B 855 TYR 0.054 0.002 TYR A 284 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7811 (tptt) cc_final: 0.7103 (ttpt) REVERT: A 222 LYS cc_start: 0.7553 (mttt) cc_final: 0.6980 (mtpt) REVERT: A 232 GLU cc_start: 0.3467 (tt0) cc_final: 0.3259 (mt-10) REVERT: A 284 TYR cc_start: 0.5137 (OUTLIER) cc_final: 0.4525 (p90) REVERT: A 305 LYS cc_start: 0.6187 (pttp) cc_final: 0.5661 (mtmm) REVERT: A 309 LYS cc_start: 0.5881 (mtpt) cc_final: 0.5335 (mppt) REVERT: A 325 GLU cc_start: 0.7366 (pm20) cc_final: 0.6930 (pm20) REVERT: A 397 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.5246 (mtm-85) REVERT: A 440 GLN cc_start: 0.7424 (mt0) cc_final: 0.7121 (mm110) REVERT: A 441 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7078 (pttm) REVERT: A 452 LYS cc_start: 0.7384 (mtpp) cc_final: 0.7172 (mtmm) REVERT: A 472 LYS cc_start: 0.7027 (ttpt) cc_final: 0.6709 (ttmm) REVERT: A 475 GLN cc_start: 0.7360 (mm-40) cc_final: 0.7105 (mm110) REVERT: A 523 ARG cc_start: 0.6712 (ttm-80) cc_final: 0.6503 (tpt-90) REVERT: A 617 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6963 (pp) REVERT: A 634 GLU cc_start: 0.6948 (tt0) cc_final: 0.6404 (tm-30) REVERT: B 192 LYS cc_start: 0.6425 (ptpt) cc_final: 0.5649 (tptt) REVERT: B 434 GLU cc_start: 0.6818 (mp0) cc_final: 0.6531 (mp0) REVERT: B 558 TYR cc_start: 0.8204 (p90) cc_final: 0.7894 (p90) REVERT: B 642 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7835 (mtpp) REVERT: B 688 GLU cc_start: 0.6961 (mp0) cc_final: 0.6338 (mp0) REVERT: B 739 LYS cc_start: 0.6452 (mttt) cc_final: 0.6189 (mtpt) REVERT: B 830 LYS cc_start: 0.7459 (pttt) cc_final: 0.7041 (pttm) outliers start: 32 outliers final: 9 residues processed: 190 average time/residue: 2.4343 time to fit residues: 501.1976 Evaluate side-chains 151 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 683 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.0060 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 445 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10821 Z= 0.228 Angle : 0.630 8.223 14569 Z= 0.343 Chirality : 0.043 0.213 1523 Planarity : 0.004 0.043 1914 Dihedral : 6.491 36.073 1442 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.03 % Allowed : 16.34 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.79 (0.22), residues: 1313 helix: -1.39 (0.26), residues: 339 sheet: 0.67 (0.44), residues: 125 loop : -1.45 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 286 HIS 0.006 0.002 HIS B 450 PHE 0.018 0.002 PHE B 855 TYR 0.058 0.002 TYR A 284 ARG 0.004 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7667 (tptt) cc_final: 0.7046 (ttmt) REVERT: A 222 LYS cc_start: 0.7619 (mttt) cc_final: 0.7071 (mtmt) REVERT: A 268 LYS cc_start: 0.7516 (mmmt) cc_final: 0.7170 (mtmt) REVERT: A 305 LYS cc_start: 0.6175 (pttp) cc_final: 0.5607 (mtmm) REVERT: A 309 LYS cc_start: 0.6032 (mtpt) cc_final: 0.5411 (mppt) REVERT: A 325 GLU cc_start: 0.7468 (pm20) cc_final: 0.7030 (pm20) REVERT: A 452 LYS cc_start: 0.7271 (mtpp) cc_final: 0.7062 (mtmm) REVERT: A 472 LYS cc_start: 0.7073 (ttpt) cc_final: 0.6782 (ttmm) REVERT: A 511 LEU cc_start: 0.7865 (mp) cc_final: 0.7588 (tt) REVERT: A 617 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.6970 (pp) REVERT: A 640 GLU cc_start: 0.7576 (tt0) cc_final: 0.7077 (mp0) REVERT: A 671 ASN cc_start: 0.7622 (m-40) cc_final: 0.7179 (t0) REVERT: B 177 LYS cc_start: 0.6662 (ttmt) cc_final: 0.6185 (tmmt) REVERT: B 190 ARG cc_start: 0.4824 (ptm-80) cc_final: 0.4072 (mtp180) REVERT: B 192 LYS cc_start: 0.6514 (ptpt) cc_final: 0.5539 (tptt) REVERT: B 283 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7013 (tt) REVERT: B 360 GLN cc_start: 0.5668 (OUTLIER) cc_final: 0.5398 (tt0) REVERT: B 449 SER cc_start: 0.7820 (t) cc_final: 0.7136 (m) REVERT: B 642 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7783 (mmmt) REVERT: B 688 GLU cc_start: 0.6948 (mp0) cc_final: 0.6325 (mp0) REVERT: B 739 LYS cc_start: 0.6623 (mttt) cc_final: 0.6327 (mtpt) REVERT: B 830 LYS cc_start: 0.7514 (pttt) cc_final: 0.7038 (pttm) outliers start: 35 outliers final: 15 residues processed: 173 average time/residue: 2.1937 time to fit residues: 414.0340 Evaluate side-chains 155 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 590 HIS ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 565 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10821 Z= 0.406 Angle : 0.727 8.413 14569 Z= 0.397 Chirality : 0.047 0.234 1523 Planarity : 0.005 0.059 1914 Dihedral : 6.992 39.872 1442 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.24 % Allowed : 17.11 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.32 (0.21), residues: 1313 helix: -1.55 (0.25), residues: 346 sheet: 0.34 (0.44), residues: 126 loop : -1.93 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 427 HIS 0.009 0.002 HIS B 450 PHE 0.021 0.003 PHE B 229 TYR 0.061 0.003 TYR A 284 ARG 0.004 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7653 (tptt) cc_final: 0.7010 (ttmm) REVERT: A 222 LYS cc_start: 0.7739 (mttt) cc_final: 0.7121 (mtmt) REVERT: A 268 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7260 (mtmt) REVERT: A 274 LYS cc_start: 0.6694 (tptm) cc_final: 0.6466 (tptt) REVERT: A 283 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6155 (tp30) REVERT: A 284 TYR cc_start: 0.5348 (OUTLIER) cc_final: 0.5038 (p90) REVERT: A 305 LYS cc_start: 0.6156 (pttp) cc_final: 0.5869 (ptpp) REVERT: A 309 LYS cc_start: 0.6118 (mtpt) cc_final: 0.5419 (mppt) REVERT: A 325 GLU cc_start: 0.7711 (pm20) cc_final: 0.7226 (pm20) REVERT: A 336 GLU cc_start: 0.7334 (mp0) cc_final: 0.7103 (mp0) REVERT: A 420 ASP cc_start: 0.6241 (OUTLIER) cc_final: 0.4983 (m-30) REVERT: A 452 LYS cc_start: 0.7316 (mtpp) cc_final: 0.7112 (mtmm) REVERT: A 472 LYS cc_start: 0.7056 (ttpt) cc_final: 0.6579 (tppt) REVERT: A 501 GLU cc_start: 0.6796 (tp30) cc_final: 0.6583 (tm-30) REVERT: A 640 GLU cc_start: 0.7628 (tt0) cc_final: 0.7102 (mp0) REVERT: A 702 ARG cc_start: 0.5121 (mmp80) cc_final: 0.4293 (mtm-85) REVERT: B 177 LYS cc_start: 0.6770 (ttmt) cc_final: 0.6211 (ttpp) REVERT: B 190 ARG cc_start: 0.5043 (ptm-80) cc_final: 0.4115 (mtp180) REVERT: B 283 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7401 (tt) REVERT: B 360 GLN cc_start: 0.5723 (OUTLIER) cc_final: 0.5467 (tt0) REVERT: B 633 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.5164 (p90) REVERT: B 642 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7991 (mtpt) REVERT: B 688 GLU cc_start: 0.6948 (mp0) cc_final: 0.6318 (mp0) REVERT: B 739 LYS cc_start: 0.6644 (mttt) cc_final: 0.6366 (mtpt) REVERT: B 826 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: B 830 LYS cc_start: 0.7569 (pttt) cc_final: 0.7026 (pttm) outliers start: 49 outliers final: 25 residues processed: 170 average time/residue: 2.2546 time to fit residues: 418.8609 Evaluate side-chains 167 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 826 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 590 HIS ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN B 841 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10821 Z= 0.171 Angle : 0.575 9.886 14569 Z= 0.311 Chirality : 0.041 0.187 1523 Planarity : 0.003 0.049 1914 Dihedral : 6.231 35.698 1442 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.54 % Allowed : 17.63 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.03 (0.21), residues: 1313 helix: -1.06 (0.27), residues: 339 sheet: 0.60 (0.47), residues: 117 loop : -1.85 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 286 HIS 0.005 0.001 HIS B 450 PHE 0.011 0.001 PHE A 390 TYR 0.049 0.001 TYR A 284 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7641 (tptt) cc_final: 0.7041 (ttmm) REVERT: A 222 LYS cc_start: 0.7728 (mttt) cc_final: 0.7098 (mtmt) REVERT: A 268 LYS cc_start: 0.7491 (mmmt) cc_final: 0.7210 (mtmt) REVERT: A 283 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6335 (tp30) REVERT: A 284 TYR cc_start: 0.4763 (OUTLIER) cc_final: 0.4363 (p90) REVERT: A 305 LYS cc_start: 0.6157 (pttp) cc_final: 0.5838 (ptpp) REVERT: A 309 LYS cc_start: 0.6007 (mtpt) cc_final: 0.5381 (mppt) REVERT: A 325 GLU cc_start: 0.7562 (pm20) cc_final: 0.7138 (pm20) REVERT: A 344 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6859 (mp) REVERT: A 386 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6956 (tttt) REVERT: A 452 LYS cc_start: 0.7200 (mtpp) cc_final: 0.6957 (mtmm) REVERT: A 472 LYS cc_start: 0.7071 (ttpt) cc_final: 0.6626 (ttmm) REVERT: A 501 GLU cc_start: 0.6565 (tp30) cc_final: 0.6342 (tm-30) REVERT: A 640 GLU cc_start: 0.7582 (tt0) cc_final: 0.7061 (mp0) REVERT: B 177 LYS cc_start: 0.6714 (ttmt) cc_final: 0.6136 (ttpp) REVERT: B 190 ARG cc_start: 0.4927 (ptm-80) cc_final: 0.4148 (mtp180) REVERT: B 283 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7043 (tt) REVERT: B 360 GLN cc_start: 0.5643 (OUTLIER) cc_final: 0.5359 (tt0) REVERT: B 372 LEU cc_start: 0.5106 (OUTLIER) cc_final: 0.4879 (tp) REVERT: B 449 SER cc_start: 0.8001 (t) cc_final: 0.7307 (m) REVERT: B 633 TYR cc_start: 0.5401 (OUTLIER) cc_final: 0.4858 (p90) REVERT: B 642 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7729 (mmmt) REVERT: B 667 ASN cc_start: 0.6396 (t0) cc_final: 0.6003 (t0) REVERT: B 688 GLU cc_start: 0.6864 (mp0) cc_final: 0.6222 (mp0) REVERT: B 739 LYS cc_start: 0.6592 (mttt) cc_final: 0.6295 (mtpt) REVERT: B 830 LYS cc_start: 0.7545 (pttt) cc_final: 0.7054 (pttm) outliers start: 41 outliers final: 20 residues processed: 163 average time/residue: 2.2191 time to fit residues: 394.9887 Evaluate side-chains 163 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN A 684 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10821 Z= 0.348 Angle : 0.665 8.877 14569 Z= 0.362 Chirality : 0.045 0.213 1523 Planarity : 0.004 0.046 1914 Dihedral : 6.590 37.985 1442 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.24 % Allowed : 17.89 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.21 (0.21), residues: 1313 helix: -1.22 (0.26), residues: 347 sheet: 0.47 (0.45), residues: 126 loop : -2.00 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 427 HIS 0.007 0.002 HIS A 590 PHE 0.017 0.002 PHE B 855 TYR 0.057 0.002 TYR A 284 ARG 0.003 0.001 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7638 (tptt) cc_final: 0.7028 (ttmm) REVERT: A 197 ASN cc_start: 0.7615 (p0) cc_final: 0.7381 (p0) REVERT: A 203 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 222 LYS cc_start: 0.7733 (mttt) cc_final: 0.7079 (mtpt) REVERT: A 268 LYS cc_start: 0.7505 (mmmt) cc_final: 0.7209 (mtmt) REVERT: A 283 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6181 (tp30) REVERT: A 284 TYR cc_start: 0.5308 (OUTLIER) cc_final: 0.4962 (p90) REVERT: A 305 LYS cc_start: 0.6122 (pttp) cc_final: 0.5774 (ptpp) REVERT: A 309 LYS cc_start: 0.6112 (mtpt) cc_final: 0.5438 (mppt) REVERT: A 325 GLU cc_start: 0.7713 (pm20) cc_final: 0.7186 (pm20) REVERT: A 336 GLU cc_start: 0.7317 (mp0) cc_final: 0.7092 (mp0) REVERT: A 386 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6989 (tttt) REVERT: A 452 LYS cc_start: 0.7349 (mtpp) cc_final: 0.7072 (mtmm) REVERT: A 472 LYS cc_start: 0.7053 (ttpt) cc_final: 0.6562 (tppt) REVERT: A 501 GLU cc_start: 0.6773 (tp30) cc_final: 0.6559 (tm-30) REVERT: A 511 LEU cc_start: 0.8128 (mp) cc_final: 0.7895 (mm) REVERT: A 617 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.6894 (pp) REVERT: A 640 GLU cc_start: 0.7626 (tt0) cc_final: 0.7325 (mt-10) REVERT: B 177 LYS cc_start: 0.6824 (ttmt) cc_final: 0.6245 (ttpp) REVERT: B 190 ARG cc_start: 0.5099 (ptm-80) cc_final: 0.4131 (mtp180) REVERT: B 283 LEU cc_start: 0.7587 (tt) cc_final: 0.7347 (tt) REVERT: B 360 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.5451 (tt0) REVERT: B 372 LEU cc_start: 0.5033 (OUTLIER) cc_final: 0.4789 (tp) REVERT: B 498 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6175 (mmpt) REVERT: B 633 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.5091 (p90) REVERT: B 642 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7707 (mmmt) REVERT: B 661 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6387 (t0) REVERT: B 688 GLU cc_start: 0.6936 (mp0) cc_final: 0.6268 (mp0) REVERT: B 830 LYS cc_start: 0.7463 (pttt) cc_final: 0.6918 (pttm) outliers start: 49 outliers final: 27 residues processed: 167 average time/residue: 2.1696 time to fit residues: 396.4800 Evaluate side-chains 169 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN B 468 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10821 Z= 0.178 Angle : 0.557 10.500 14569 Z= 0.300 Chirality : 0.041 0.184 1523 Planarity : 0.003 0.042 1914 Dihedral : 5.951 34.568 1440 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.63 % Allowed : 18.76 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.93 (0.22), residues: 1313 helix: -0.84 (0.27), residues: 346 sheet: 0.74 (0.48), residues: 117 loop : -1.88 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.010 0.002 HIS A 590 PHE 0.010 0.001 PHE B 855 TYR 0.047 0.001 TYR A 284 ARG 0.003 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7624 (tptt) cc_final: 0.7071 (ttmm) REVERT: A 222 LYS cc_start: 0.7715 (mttt) cc_final: 0.7029 (mtpt) REVERT: A 268 LYS cc_start: 0.7523 (mmmt) cc_final: 0.7215 (mtmt) REVERT: A 283 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6288 (tp30) REVERT: A 284 TYR cc_start: 0.4700 (OUTLIER) cc_final: 0.4281 (p90) REVERT: A 305 LYS cc_start: 0.6106 (pttp) cc_final: 0.5778 (ptpp) REVERT: A 309 LYS cc_start: 0.6032 (mtpt) cc_final: 0.5367 (mppt) REVERT: A 325 GLU cc_start: 0.7548 (pm20) cc_final: 0.7122 (pm20) REVERT: A 336 GLU cc_start: 0.7402 (mp0) cc_final: 0.7095 (mp0) REVERT: A 344 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 386 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6955 (tttt) REVERT: A 452 LYS cc_start: 0.7195 (mtpp) cc_final: 0.6908 (mtmm) REVERT: A 472 LYS cc_start: 0.6992 (ttpt) cc_final: 0.6481 (tppt) REVERT: A 475 GLN cc_start: 0.7158 (mm110) cc_final: 0.6928 (mm110) REVERT: A 498 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.6906 (t0) REVERT: A 501 GLU cc_start: 0.6514 (tp30) cc_final: 0.6138 (tm-30) REVERT: A 511 LEU cc_start: 0.8068 (mp) cc_final: 0.7830 (mm) REVERT: A 640 GLU cc_start: 0.7582 (tt0) cc_final: 0.7219 (mt-10) REVERT: B 177 LYS cc_start: 0.6772 (ttmt) cc_final: 0.6190 (ttpp) REVERT: B 190 ARG cc_start: 0.4969 (ptm-80) cc_final: 0.4074 (mtp180) REVERT: B 283 LEU cc_start: 0.7367 (tt) cc_final: 0.7116 (tt) REVERT: B 360 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.5537 (tt0) REVERT: B 498 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6166 (mmpt) REVERT: B 633 TYR cc_start: 0.5250 (OUTLIER) cc_final: 0.4766 (p90) REVERT: B 642 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7690 (mmmt) REVERT: B 661 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6230 (t0) REVERT: B 667 ASN cc_start: 0.6471 (t0) cc_final: 0.5953 (t0) REVERT: B 688 GLU cc_start: 0.6955 (mp0) cc_final: 0.6323 (mp0) REVERT: B 830 LYS cc_start: 0.7393 (pttt) cc_final: 0.6784 (pttm) outliers start: 42 outliers final: 25 residues processed: 164 average time/residue: 2.1228 time to fit residues: 383.5420 Evaluate side-chains 167 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 828 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10821 Z= 0.237 Angle : 0.589 10.422 14569 Z= 0.318 Chirality : 0.042 0.195 1523 Planarity : 0.004 0.037 1914 Dihedral : 6.018 35.068 1440 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.94 % Allowed : 20.05 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.98 (0.22), residues: 1313 helix: -0.84 (0.27), residues: 346 sheet: 0.51 (0.47), residues: 124 loop : -1.91 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.008 0.002 HIS A 590 PHE 0.017 0.002 PHE B 716 TYR 0.052 0.002 TYR A 284 ARG 0.005 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7621 (tptt) cc_final: 0.7068 (ttmm) REVERT: A 222 LYS cc_start: 0.7676 (mttt) cc_final: 0.7001 (mtpt) REVERT: A 283 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6276 (tp30) REVERT: A 284 TYR cc_start: 0.4994 (OUTLIER) cc_final: 0.4566 (p90) REVERT: A 305 LYS cc_start: 0.6091 (pttp) cc_final: 0.5760 (ptpp) REVERT: A 309 LYS cc_start: 0.6079 (mtpt) cc_final: 0.5368 (mppt) REVERT: A 325 GLU cc_start: 0.7596 (pm20) cc_final: 0.7195 (pm20) REVERT: A 386 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6963 (tttt) REVERT: A 452 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6948 (mtmm) REVERT: A 472 LYS cc_start: 0.6941 (ttpt) cc_final: 0.6487 (ttmm) REVERT: A 475 GLN cc_start: 0.7130 (mm110) cc_final: 0.6902 (mm110) REVERT: A 498 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.6743 (t0) REVERT: A 501 GLU cc_start: 0.6595 (tp30) cc_final: 0.6135 (tm-30) REVERT: A 511 LEU cc_start: 0.8087 (mp) cc_final: 0.7835 (mm) REVERT: A 640 GLU cc_start: 0.7626 (tt0) cc_final: 0.7335 (mt-10) REVERT: B 177 LYS cc_start: 0.6816 (ttmt) cc_final: 0.6232 (ttpp) REVERT: B 190 ARG cc_start: 0.5068 (ptm-80) cc_final: 0.4131 (mtp180) REVERT: B 283 LEU cc_start: 0.7449 (tt) cc_final: 0.7218 (tt) REVERT: B 360 GLN cc_start: 0.5854 (OUTLIER) cc_final: 0.5581 (tt0) REVERT: B 498 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6177 (mmpt) REVERT: B 633 TYR cc_start: 0.5423 (OUTLIER) cc_final: 0.5104 (p90) REVERT: B 642 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7715 (mmmt) REVERT: B 661 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6361 (t0) REVERT: B 688 GLU cc_start: 0.6960 (mp0) cc_final: 0.6305 (mp0) REVERT: B 830 LYS cc_start: 0.7435 (pttt) cc_final: 0.6836 (pttm) outliers start: 34 outliers final: 24 residues processed: 156 average time/residue: 2.1491 time to fit residues: 367.9759 Evaluate side-chains 167 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10821 Z= 0.294 Angle : 0.630 9.679 14569 Z= 0.340 Chirality : 0.043 0.203 1523 Planarity : 0.004 0.038 1914 Dihedral : 6.184 35.957 1440 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.46 % Allowed : 19.71 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.08 (0.21), residues: 1313 helix: -0.96 (0.27), residues: 346 sheet: 0.57 (0.46), residues: 126 loop : -1.99 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 427 HIS 0.007 0.002 HIS A 590 PHE 0.018 0.002 PHE B 716 TYR 0.053 0.002 TYR A 284 ARG 0.002 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7631 (tptt) cc_final: 0.7067 (ttmm) REVERT: A 222 LYS cc_start: 0.7619 (mttt) cc_final: 0.6969 (mtpt) REVERT: A 268 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7288 (mtmt) REVERT: A 283 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6286 (tp30) REVERT: A 284 TYR cc_start: 0.5103 (OUTLIER) cc_final: 0.4718 (p90) REVERT: A 291 LEU cc_start: 0.7391 (mp) cc_final: 0.7145 (tp) REVERT: A 305 LYS cc_start: 0.6101 (pttp) cc_final: 0.5771 (ptpp) REVERT: A 309 LYS cc_start: 0.6065 (mtpt) cc_final: 0.5363 (mppt) REVERT: A 325 GLU cc_start: 0.7647 (pm20) cc_final: 0.7225 (pm20) REVERT: A 386 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6972 (tttt) REVERT: A 452 LYS cc_start: 0.7325 (mtpp) cc_final: 0.6984 (mtmm) REVERT: A 472 LYS cc_start: 0.6978 (ttpt) cc_final: 0.6535 (tppt) REVERT: A 498 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.6697 (t0) REVERT: A 501 GLU cc_start: 0.6736 (tp30) cc_final: 0.6241 (tm-30) REVERT: A 511 LEU cc_start: 0.8102 (mp) cc_final: 0.7851 (mm) REVERT: A 617 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.6869 (pp) REVERT: A 640 GLU cc_start: 0.7618 (tt0) cc_final: 0.7255 (mt-10) REVERT: B 177 LYS cc_start: 0.6889 (ttmt) cc_final: 0.6265 (ttpp) REVERT: B 190 ARG cc_start: 0.5116 (ptm-80) cc_final: 0.4060 (mtp180) REVERT: B 283 LEU cc_start: 0.7520 (tt) cc_final: 0.7297 (tt) REVERT: B 360 GLN cc_start: 0.5862 (OUTLIER) cc_final: 0.5616 (tt0) REVERT: B 498 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6146 (mmpt) REVERT: B 633 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.5190 (p90) REVERT: B 642 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7723 (mmmt) REVERT: B 661 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6363 (t0) REVERT: B 688 GLU cc_start: 0.6945 (mp0) cc_final: 0.6278 (mp0) REVERT: B 830 LYS cc_start: 0.7419 (pttt) cc_final: 0.6814 (pttm) outliers start: 40 outliers final: 22 residues processed: 158 average time/residue: 2.1443 time to fit residues: 371.6567 Evaluate side-chains 165 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 828 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 110 optimal weight: 0.0040 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 563 ASN B 468 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10821 Z= 0.201 Angle : 0.577 10.150 14569 Z= 0.308 Chirality : 0.041 0.189 1523 Planarity : 0.003 0.039 1914 Dihedral : 5.889 34.161 1440 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.03 % Allowed : 20.05 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.94 (0.22), residues: 1313 helix: -0.77 (0.27), residues: 346 sheet: 0.55 (0.47), residues: 124 loop : -1.91 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.009 0.002 HIS A 590 PHE 0.014 0.001 PHE B 716 TYR 0.047 0.002 TYR A 284 ARG 0.002 0.000 ARG B 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7622 (tptt) cc_final: 0.7084 (ttmm) REVERT: A 203 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7879 (m) REVERT: A 222 LYS cc_start: 0.7632 (mttt) cc_final: 0.6921 (mtpt) REVERT: A 268 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7245 (mtmt) REVERT: A 283 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6328 (tp30) REVERT: A 284 TYR cc_start: 0.4770 (OUTLIER) cc_final: 0.4346 (p90) REVERT: A 305 LYS cc_start: 0.6070 (pttp) cc_final: 0.5745 (ptpp) REVERT: A 309 LYS cc_start: 0.6019 (mtpt) cc_final: 0.5328 (mppt) REVERT: A 325 GLU cc_start: 0.7593 (pm20) cc_final: 0.7153 (pm20) REVERT: A 386 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6956 (tttt) REVERT: A 472 LYS cc_start: 0.6813 (ttpt) cc_final: 0.6405 (ttmm) REVERT: A 498 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.6802 (t0) REVERT: A 501 GLU cc_start: 0.6587 (tp30) cc_final: 0.6128 (tm-30) REVERT: A 511 LEU cc_start: 0.8131 (mp) cc_final: 0.7890 (mm) REVERT: A 617 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.6867 (pp) REVERT: A 640 GLU cc_start: 0.7555 (tt0) cc_final: 0.7218 (mt-10) REVERT: B 177 LYS cc_start: 0.6877 (ttmt) cc_final: 0.6278 (ttpp) REVERT: B 190 ARG cc_start: 0.5140 (ptm-80) cc_final: 0.4169 (mtp180) REVERT: B 283 LEU cc_start: 0.7435 (tt) cc_final: 0.7212 (tt) REVERT: B 360 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5578 (tt0) REVERT: B 449 SER cc_start: 0.8123 (t) cc_final: 0.7516 (m) REVERT: B 633 TYR cc_start: 0.5313 (OUTLIER) cc_final: 0.5057 (p90) REVERT: B 642 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7700 (mmmt) REVERT: B 661 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6227 (t0) REVERT: B 688 GLU cc_start: 0.6956 (mp0) cc_final: 0.6303 (mp0) REVERT: B 830 LYS cc_start: 0.7395 (pttt) cc_final: 0.6794 (pttm) outliers start: 35 outliers final: 23 residues processed: 155 average time/residue: 2.1711 time to fit residues: 368.3733 Evaluate side-chains 162 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 828 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN B 468 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.230330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.202278 restraints weight = 34096.641| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.86 r_work: 0.4319 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4226 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 10821 Z= 0.286 Angle : 0.845 59.195 14569 Z= 0.500 Chirality : 0.041 0.189 1523 Planarity : 0.003 0.038 1914 Dihedral : 5.910 34.130 1440 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.28 % Allowed : 20.05 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.94 (0.22), residues: 1313 helix: -0.77 (0.27), residues: 346 sheet: 0.55 (0.47), residues: 124 loop : -1.91 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.008 0.002 HIS A 590 PHE 0.014 0.001 PHE B 716 TYR 0.048 0.002 TYR A 284 ARG 0.002 0.000 ARG A 580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7732.29 seconds wall clock time: 135 minutes 25.90 seconds (8125.90 seconds total)