Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 19:18:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/04_2023/7adk_11729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/04_2023/7adk_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_11729/04_2023/7adk_11729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/04_2023/7adk_11729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/04_2023/7adk_11729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adk_11729/04_2023/7adk_11729.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 8.85, per 1000 atoms: 0.42 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: 16.31 Conformation dependent library (CDL) restraints added in 1.7 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: 0.81 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: 7.96 Time building geometry restraints manager: 16.57 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: 7660 17.72 - 35.44: 646 35.44 - 53.16: 124 53.16 - 70.89: 81 70.89 - 88.61: 18 Dihedral angle restraints: 8529 sinusoidal: 3929 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 8526 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: 1.030 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: 0.300 Extract box with map and model: 5.580 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 63.230 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.070 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.652 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 outliers start: 5 outliers final: 3 residues processed: 249 average time/residue: 2.4004 time to fit residues: 648.5852 Evaluate side-chains 147 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.3882 time to fit residues: 2.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.9990 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: 0.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10821 Z= 0.216 Angle : 0.687 8.243 14569 Z= 0.371 Chirality : 0.044 0.205 1523 Planarity : 0.004 0.045 1914 Dihedral : 7.159 36.979 1438 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -1.86 (0.25), residues: 331 sheet: 0.47 (0.43), residues: 120 loop : -1.35 (0.21), residues: 862 *********************** 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 202 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 183 average time/residue: 2.3451 time to fit residues: 467.2341 Evaluate side-chains 139 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.2777 time to fit residues: 4.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 445 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 HIS ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 450 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 10821 Z= 0.397 Angle : 0.759 9.245 14569 Z= 0.415 Chirality : 0.048 0.241 1523 Planarity : 0.005 0.060 1914 Dihedral : 7.145 40.882 1438 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer Outliers : 4.75 % 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: -2.20 (0.21), residues: 1313 helix: -1.69 (0.25), residues: 347 sheet: 0.77 (0.45), residues: 115 loop : -1.77 (0.20), residues: 851 *********************** 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 195 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 140 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 31 residues processed: 173 average time/residue: 2.0824 time to fit residues: 396.5911 Evaluate side-chains 155 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 12 average time/residue: 0.6231 time to fit residues: 11.9958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 633 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10821 Z= 0.173 Angle : 0.581 9.523 14569 Z= 0.313 Chirality : 0.041 0.197 1523 Planarity : 0.003 0.045 1914 Dihedral : 6.255 35.226 1438 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer Outliers : 3.80 % 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: -1.97 (0.22), residues: 1313 helix: -1.28 (0.26), residues: 342 sheet: 0.70 (0.49), residues: 111 loop : -1.68 (0.20), residues: 860 *********************** 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 186 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 27 residues processed: 173 average time/residue: 2.0780 time to fit residues: 395.7244 Evaluate side-chains 154 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.644 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 21 residues processed: 9 average time/residue: 0.5361 time to fit residues: 8.6210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 458 ASN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10821 Z= 0.278 Angle : 0.641 8.785 14569 Z= 0.345 Chirality : 0.043 0.221 1523 Planarity : 0.004 0.045 1914 Dihedral : 6.329 36.562 1438 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 4.41 % 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: -2.13 (0.21), residues: 1313 helix: -1.14 (0.26), residues: 346 sheet: 0.54 (0.45), residues: 128 loop : -1.96 (0.20), residues: 839 *********************** 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 179 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 33 residues processed: 162 average time/residue: 2.0473 time to fit residues: 366.8844 Evaluate side-chains 160 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 11 average time/residue: 0.4905 time to fit residues: 9.7873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN A 563 ASN ** 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 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10821 Z= 0.242 Angle : 0.608 9.834 14569 Z= 0.327 Chirality : 0.042 0.199 1523 Planarity : 0.004 0.044 1914 Dihedral : 6.176 35.907 1438 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer Outliers : 4.15 % 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: -2.10 (0.21), residues: 1313 helix: -1.06 (0.26), residues: 354 sheet: 0.62 (0.45), residues: 126 loop : -1.98 (0.19), residues: 833 *********************** 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 177 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 129 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 27 residues processed: 159 average time/residue: 1.9925 time to fit residues: 351.3391 Evaluate side-chains 151 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 10 average time/residue: 1.2941 time to fit residues: 19.0722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 76 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 563 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10821 Z= 0.221 Angle : 0.593 9.460 14569 Z= 0.317 Chirality : 0.041 0.205 1523 Planarity : 0.003 0.040 1914 Dihedral : 5.992 35.364 1438 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 3.63 % 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: -2.07 (0.21), residues: 1313 helix: -0.99 (0.26), residues: 348 sheet: 0.81 (0.48), residues: 117 loop : -1.97 (0.19), residues: 848 *********************** 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 173 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 31 residues processed: 155 average time/residue: 1.9720 time to fit residues: 338.4821 Evaluate side-chains 154 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 10 average time/residue: 0.5034 time to fit residues: 9.5142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 563 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 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** B 775 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10821 Z= 0.258 Angle : 0.608 10.019 14569 Z= 0.328 Chirality : 0.042 0.209 1523 Planarity : 0.004 0.038 1914 Dihedral : 6.071 35.870 1438 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer Outliers : 3.63 % 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: -2.12 (0.21), residues: 1313 helix: -1.01 (0.26), residues: 348 sheet: 0.66 (0.46), residues: 126 loop : -2.03 (0.19), residues: 839 *********************** 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 165 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 148 average time/residue: 1.9573 time to fit residues: 322.4855 Evaluate side-chains 145 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 7 average time/residue: 0.5492 time to fit residues: 7.5454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 563 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10821 Z= 0.235 Angle : 0.598 9.445 14569 Z= 0.320 Chirality : 0.041 0.180 1523 Planarity : 0.003 0.033 1914 Dihedral : 5.960 34.838 1438 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer Outliers : 3.28 % 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: -2.07 (0.21), residues: 1313 helix: -0.90 (0.27), residues: 342 sheet: 0.74 (0.46), residues: 125 loop : -2.03 (0.19), residues: 846 *********************** 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 161 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 30 residues processed: 148 average time/residue: 1.9730 time to fit residues: 324.3144 Evaluate side-chains 149 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 10 average time/residue: 0.7004 time to fit residues: 11.2132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 440 GLN A 563 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.5405 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= 0.214 Angle : 0.579 10.702 14569 Z= 0.311 Chirality : 0.041 0.163 1523 Planarity : 0.003 0.031 1914 Dihedral : 5.854 34.245 1438 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer Outliers : 2.33 % 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: -2.02 (0.22), residues: 1313 helix: -0.82 (0.27), residues: 342 sheet: 0.73 (0.46), residues: 125 loop : -2.01 (0.19), residues: 846 ********************** 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 155 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 24 residues processed: 151 average time/residue: 2.0094 time to fit residues: 336.7686 Evaluate side-chains 145 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 4 average time/residue: 0.6924 time to fit residues: 5.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.0070 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 440 GLN A 563 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.238995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.212925 restraints weight = 33903.365| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 1.68 r_work: 0.4403 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4298 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10821 Z= 0.168 Angle : 0.555 10.458 14569 Z= 0.294 Chirality : 0.040 0.150 1523 Planarity : 0.003 0.030 1914 Dihedral : 5.579 32.439 1438 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 2.77 % 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: -1.87 (0.22), residues: 1313 helix: -0.66 (0.28), residues: 342 sheet: 0.94 (0.49), residues: 116 loop : -1.92 (0.20), residues: 855 =============================================================================== Job complete usr+sys time: 7518.88 seconds wall clock time: 132 minutes 36.18 seconds (7956.18 seconds total)