Starting phenix.real_space_refine on Fri Feb 16 06:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu3_28603/02_2024/8eu3_28603_neut_updated.pdb" } resolution = 3.62 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= 0.003 sd= 0.072 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 P 4 5.49 5 S 66 5.16 5 C 9511 2.51 5 N 2378 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 583": "OD1" <-> "OD2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C ASP 609": "OD1" <-> "OD2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 257": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ASP 461": "OD1" <-> "OD2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 494": "OD1" <-> "OD2" Residue "D ASP 513": "OD1" <-> "OD2" Residue "D ASP 523": "OD1" <-> "OD2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D GLU 626": "OE1" <-> "OE2" Residue "D ASP 633": "OD1" <-> "OD2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3631 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 bond proxies already assigned to first conformer: 3695 Chain: "B" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3616 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3624 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 14, 'TRANS': 430} Chain breaks: 1 Chain: "D" Number of atoms: 3591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 bond proxies already assigned to first conformer: 3663 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.30, per 1000 atoms: 0.77 Number of scatterers: 14596 At special positions: 0 Unit cell: (132.25, 108.974, 106.858, 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 66 16.00 P 4 15.00 O 2637 8.00 N 2378 7.00 C 9511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 4.0 seconds 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3358 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 60.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 167 through 192 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 200 through 221 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.552A pdb=" N ARG A 274 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 298 through 328 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 375 through 427 removed outlier: 4.806A pdb=" N SER A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ARG A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 488 through 497 Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 581 through 590 removed outlier: 3.825A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 608 Processing helix chain 'B' and resid 166 through 192 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 200 through 222 Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 271 through 279 removed outlier: 3.838A pdb=" N ARG B 274 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 298 through 328 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 375 through 405 Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 431 through 447 Processing helix chain 'B' and resid 453 through 456 No H-bonds generated for 'chain 'B' and resid 453 through 456' Processing helix chain 'B' and resid 462 through 477 removed outlier: 5.044A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 592 through 609 Processing helix chain 'C' and resid 167 through 192 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 195 through 198 No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 200 through 221 Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 248 through 255 Processing helix chain 'C' and resid 271 through 279 removed outlier: 3.763A pdb=" N PHE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 298 through 328 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 375 through 406 Processing helix chain 'C' and resid 408 through 427 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 453 through 459 removed outlier: 5.377A pdb=" N SER C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 477 removed outlier: 5.422A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 592 through 608 Processing helix chain 'D' and resid 216 through 241 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 250 through 269 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.545A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.839A pdb=" N LEU D 315 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 317 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 4.284A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.606A pdb=" N PHE D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 378 Processing helix chain 'D' and resid 393 through 405 Processing helix chain 'D' and resid 417 through 448 Processing helix chain 'D' and resid 450 through 468 Processing helix chain 'D' and resid 473 through 490 Processing helix chain 'D' and resid 496 through 499 No H-bonds generated for 'chain 'D' and resid 496 through 499' Processing helix chain 'D' and resid 504 through 520 removed outlier: 3.596A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 526 No H-bonds generated for 'chain 'D' and resid 524 through 526' Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 593 through 596 No H-bonds generated for 'chain 'D' and resid 593 through 596' Processing helix chain 'D' and resid 621 through 630 removed outlier: 4.097A pdb=" N HIS D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 645 Processing sheet with id= A, first strand: chain 'A' and resid 226 through 228 removed outlier: 4.143A pdb=" N PHE A 226 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 518 through 522 Processing sheet with id= C, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.902A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 499 through 503 Processing sheet with id= E, first strand: chain 'C' and resid 499 through 502 Processing sheet with id= F, first strand: chain 'C' and resid 527 through 530 Processing sheet with id= G, first strand: chain 'D' and resid 560 through 564 Processing sheet with id= H, first strand: chain 'D' and resid 607 through 610 removed outlier: 3.569A pdb=" N VAL D 569 " --> pdb=" O LEU D 584 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2299 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: 4.02 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4341 1.34 - 1.46: 2764 1.46 - 1.57: 7736 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14946 Sorted by residual: bond pdb=" C2' PCG B 802 " pdb=" C3' PCG B 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.41e+02 bond pdb=" C2' PCG C 802 " pdb=" C3' PCG C 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.41e+02 bond pdb=" C2' PCG A 802 " pdb=" C3' PCG A 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C2' PCG D 901 " pdb=" C3' PCG D 901 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " ideal model delta sigma weight residual 1.808 1.532 0.276 2.00e-02 2.50e+03 1.90e+02 ... (remaining 14941 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.72: 266 105.72 - 113.76: 8430 113.76 - 121.79: 8842 121.79 - 129.83: 2649 129.83 - 137.87: 101 Bond angle restraints: 20288 Sorted by residual: angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 128.25 -16.02 3.00e+00 1.11e-01 2.85e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 112.23 127.96 -15.73 3.00e+00 1.11e-01 2.75e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 112.23 127.89 -15.66 3.00e+00 1.11e-01 2.73e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 112.23 127.88 -15.65 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C2 PCG B 802 " pdb=" N3 PCG B 802 " pdb=" C4 PCG B 802 " ideal model delta sigma weight residual 120.18 106.84 13.34 3.00e+00 1.11e-01 1.98e+01 ... (remaining 20283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.70: 7930 18.70 - 37.39: 780 37.39 - 56.09: 118 56.09 - 74.78: 21 74.78 - 93.48: 18 Dihedral angle restraints: 8867 sinusoidal: 3642 harmonic: 5225 Sorted by residual: dihedral pdb=" CA LEU B 588 " pdb=" C LEU B 588 " pdb=" N THR B 589 " pdb=" CA THR B 589 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA VAL A 480 " pdb=" C VAL A 480 " pdb=" N ARG A 481 " pdb=" CA ARG A 481 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASP C 193 " pdb=" C ASP C 193 " pdb=" N GLU C 194 " pdb=" CA GLU C 194 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 8864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 2295 0.326 - 0.653: 5 0.653 - 0.979: 3 0.979 - 1.306: 0 1.306 - 1.632: 4 Chirality restraints: 2307 Sorted by residual: chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-01 2.50e+01 6.66e+01 chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.79 -1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.13e+01 ... (remaining 2304 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 392 " 0.056 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" O PHE A 392 " -0.020 2.00e-02 2.50e+03 pdb=" CA APHE A 392 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 393 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO D 273 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 236 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO D 237 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 237 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 237 " -0.041 5.00e-02 4.00e+02 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1949 2.75 - 3.29: 14386 3.29 - 3.82: 25147 3.82 - 4.36: 27461 4.36 - 4.90: 47531 Nonbonded interactions: 116474 Sorted by model distance: nonbonded pdb=" OG SER A 580 " pdb=" OD1 ASP A 582 " model vdw 2.211 2.440 nonbonded pdb=" O ASP A 162 " pdb=" OG SER A 165 " model vdw 2.289 2.440 nonbonded pdb=" O THR A 360 " pdb=" OG1 THR A 364 " model vdw 2.290 2.440 nonbonded pdb=" O TYR D 294 " pdb=" OG SER D 297 " model vdw 2.302 2.440 nonbonded pdb=" OG SER D 594 " pdb=" O ASN D 602 " model vdw 2.308 2.440 ... (remaining 116469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 259 or resid 270 through 391 or resid 393 thro \ ugh 609 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 259 or resid 270 through 391 or resid 393 thro \ ugh 609 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 259 or resid 270 through 391 or resid 393 thro \ ugh 609 or resid 801 through 802)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.120 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 45.040 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.369 14946 Z= 0.852 Angle : 1.041 16.021 20288 Z= 0.505 Chirality : 0.093 1.632 2307 Planarity : 0.007 0.079 2493 Dihedral : 15.169 93.476 5509 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.19 % Allowed : 4.90 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.15), residues: 1756 helix: -1.94 (0.11), residues: 1151 sheet: -2.82 (0.62), residues: 59 loop : -2.64 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 400 HIS 0.006 0.001 HIS D 293 PHE 0.043 0.002 PHE A 385 TYR 0.023 0.002 TYR A 184 ARG 0.008 0.001 ARG D 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 311 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8562 (tt) cc_final: 0.8358 (tt) REVERT: A 232 MET cc_start: 0.8156 (tpp) cc_final: 0.7844 (tpp) REVERT: A 241 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8040 (mp10) REVERT: A 300 MET cc_start: 0.7112 (mmm) cc_final: 0.6861 (tpt) REVERT: A 439 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8245 (mtp85) REVERT: A 467 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 478 LYS cc_start: 0.7527 (ptmt) cc_final: 0.7249 (tptp) REVERT: B 240 TRP cc_start: 0.8482 (t-100) cc_final: 0.8199 (t60) REVERT: B 254 LEU cc_start: 0.8782 (tp) cc_final: 0.8545 (tp) REVERT: B 289 ASP cc_start: 0.7464 (t0) cc_final: 0.7217 (t70) REVERT: B 314 ILE cc_start: 0.8738 (mm) cc_final: 0.8535 (mt) REVERT: B 410 ARG cc_start: 0.8068 (tpm170) cc_final: 0.7732 (tpm170) REVERT: B 414 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8353 (tp40) REVERT: B 546 TYR cc_start: 0.7618 (p90) cc_final: 0.7377 (p90) REVERT: C 200 LEU cc_start: 0.9116 (tp) cc_final: 0.8811 (tp) REVERT: C 241 GLN cc_start: 0.8618 (mm110) cc_final: 0.8368 (mm-40) REVERT: C 406 MET cc_start: 0.7798 (ttp) cc_final: 0.7548 (mtp) REVERT: C 604 GLN cc_start: 0.9081 (mt0) cc_final: 0.8800 (pp30) REVERT: D 248 ASP cc_start: 0.5907 (t0) cc_final: 0.5346 (t0) REVERT: D 250 ILE cc_start: 0.8790 (mt) cc_final: 0.8560 (mt) REVERT: D 291 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7955 (ttp-170) REVERT: D 327 ARG cc_start: 0.7620 (mpt180) cc_final: 0.7336 (mpt-90) REVERT: D 635 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7704 (tm-30) outliers start: 3 outliers final: 0 residues processed: 312 average time/residue: 0.3039 time to fit residues: 133.8561 Evaluate side-chains 221 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 471 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 229 GLN B 305 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 554 ASN B 567 ASN B 604 GLN C 242 HIS ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 340 HIS D 365 HIS D 367 ASN D 423 GLN D 426 ASN D 570 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14946 Z= 0.194 Angle : 0.606 8.920 20288 Z= 0.310 Chirality : 0.041 0.166 2307 Planarity : 0.005 0.066 2493 Dihedral : 6.913 88.663 2059 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.82 % Allowed : 11.18 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 1756 helix: -0.28 (0.14), residues: 1158 sheet: -2.27 (0.59), residues: 58 loop : -2.17 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 373 HIS 0.010 0.001 HIS C 242 PHE 0.027 0.001 PHE A 577 TYR 0.024 0.001 TYR C 184 ARG 0.004 0.000 ARG D 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8036 (mp10) REVERT: A 300 MET cc_start: 0.6961 (mmm) cc_final: 0.6750 (tpt) REVERT: A 410 ARG cc_start: 0.7284 (tpm170) cc_final: 0.6713 (tpp-160) REVERT: A 473 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6439 (t-90) REVERT: A 478 LYS cc_start: 0.7319 (ptmt) cc_final: 0.6711 (tppt) REVERT: B 240 TRP cc_start: 0.8455 (t-100) cc_final: 0.8200 (t60) REVERT: B 254 LEU cc_start: 0.8756 (tp) cc_final: 0.8497 (tp) REVERT: B 270 TYR cc_start: 0.6777 (t80) cc_final: 0.6552 (t80) REVERT: B 422 GLN cc_start: 0.8723 (tp40) cc_final: 0.8386 (tt0) REVERT: B 546 TYR cc_start: 0.7586 (p90) cc_final: 0.7328 (p90) REVERT: C 232 MET cc_start: 0.8521 (tpp) cc_final: 0.8161 (tpp) REVERT: C 313 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8521 (tt) REVERT: C 422 GLN cc_start: 0.8677 (tp40) cc_final: 0.8336 (tp40) REVERT: C 604 GLN cc_start: 0.9121 (mt0) cc_final: 0.8813 (pp30) REVERT: D 248 ASP cc_start: 0.5795 (t0) cc_final: 0.5301 (t0) REVERT: D 291 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7976 (ttp-170) REVERT: D 310 PHE cc_start: 0.8454 (m-80) cc_final: 0.8253 (m-80) REVERT: D 327 ARG cc_start: 0.7790 (mpt180) cc_final: 0.7505 (mpt-90) REVERT: D 566 HIS cc_start: 0.6879 (t70) cc_final: 0.6638 (t70) outliers start: 29 outliers final: 16 residues processed: 259 average time/residue: 0.2647 time to fit residues: 101.1706 Evaluate side-chains 238 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 0.0000 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 340 HIS D 415 GLN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14946 Z= 0.261 Angle : 0.604 9.286 20288 Z= 0.304 Chirality : 0.041 0.167 2307 Planarity : 0.004 0.057 2493 Dihedral : 6.437 79.647 2059 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.76 % Allowed : 13.00 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1756 helix: 0.50 (0.15), residues: 1151 sheet: -2.52 (0.63), residues: 54 loop : -1.82 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 373 HIS 0.009 0.001 HIS C 242 PHE 0.017 0.001 PHE C 301 TYR 0.022 0.002 TYR A 423 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 239 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7950 (mp10) REVERT: A 256 LEU cc_start: 0.8945 (tp) cc_final: 0.8695 (tp) REVERT: A 300 MET cc_start: 0.7025 (mmm) cc_final: 0.6809 (tpt) REVERT: A 410 ARG cc_start: 0.7174 (tpm170) cc_final: 0.6767 (tpp-160) REVERT: A 478 LYS cc_start: 0.7389 (ptmt) cc_final: 0.6713 (tppt) REVERT: B 175 ILE cc_start: 0.9029 (tp) cc_final: 0.8662 (tp) REVERT: B 240 TRP cc_start: 0.8464 (t-100) cc_final: 0.8203 (t60) REVERT: B 254 LEU cc_start: 0.8758 (tp) cc_final: 0.8468 (tp) REVERT: B 422 GLN cc_start: 0.8661 (tp40) cc_final: 0.8405 (tt0) REVERT: B 425 GLN cc_start: 0.8798 (tp40) cc_final: 0.8474 (tp-100) REVERT: B 546 TYR cc_start: 0.7600 (p90) cc_final: 0.7288 (p90) REVERT: C 200 LEU cc_start: 0.9144 (tp) cc_final: 0.8878 (tp) REVERT: C 232 MET cc_start: 0.8481 (tpp) cc_final: 0.8166 (tpp) REVERT: C 353 ILE cc_start: 0.8659 (mm) cc_final: 0.8314 (mt) REVERT: C 422 GLN cc_start: 0.8734 (tp40) cc_final: 0.8407 (tp40) REVERT: C 462 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8066 (t0) REVERT: D 248 ASP cc_start: 0.5640 (t0) cc_final: 0.5205 (t0) REVERT: D 291 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7998 (ttp-170) REVERT: D 352 ARG cc_start: 0.6921 (mpp80) cc_final: 0.6661 (mpp80) REVERT: D 566 HIS cc_start: 0.6936 (t70) cc_final: 0.6637 (t70) outliers start: 44 outliers final: 25 residues processed: 262 average time/residue: 0.2634 time to fit residues: 101.3903 Evaluate side-chains 257 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 231 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 82 optimal weight: 0.0030 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14946 Z= 0.159 Angle : 0.549 9.176 20288 Z= 0.277 Chirality : 0.039 0.149 2307 Planarity : 0.004 0.058 2493 Dihedral : 6.099 81.448 2059 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.51 % Allowed : 15.01 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1756 helix: 0.99 (0.15), residues: 1150 sheet: -2.57 (0.65), residues: 54 loop : -1.56 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 373 HIS 0.014 0.001 HIS C 242 PHE 0.030 0.001 PHE D 310 TYR 0.023 0.001 TYR A 423 ARG 0.010 0.000 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8016 (m-30) cc_final: 0.7810 (m-30) REVERT: A 241 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7925 (mp10) REVERT: A 256 LEU cc_start: 0.9021 (tp) cc_final: 0.8800 (tp) REVERT: A 410 ARG cc_start: 0.7112 (tpm170) cc_final: 0.6715 (tpp-160) REVERT: A 473 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6092 (t-90) REVERT: A 478 LYS cc_start: 0.7278 (ptmt) cc_final: 0.6696 (tppt) REVERT: B 175 ILE cc_start: 0.8965 (tp) cc_final: 0.8577 (tp) REVERT: B 240 TRP cc_start: 0.8428 (t-100) cc_final: 0.8196 (t60) REVERT: B 254 LEU cc_start: 0.8740 (tp) cc_final: 0.8447 (tp) REVERT: B 425 GLN cc_start: 0.8806 (tp40) cc_final: 0.8481 (tp-100) REVERT: B 546 TYR cc_start: 0.7541 (p90) cc_final: 0.7316 (p90) REVERT: C 422 GLN cc_start: 0.8721 (tp40) cc_final: 0.8463 (tp40) REVERT: C 462 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8009 (t0) REVERT: C 519 MET cc_start: 0.8690 (ttp) cc_final: 0.8326 (ttt) REVERT: C 580 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7806 (p) REVERT: D 248 ASP cc_start: 0.5659 (t0) cc_final: 0.5213 (t0) REVERT: D 291 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7916 (ttp-170) outliers start: 24 outliers final: 14 residues processed: 268 average time/residue: 0.2644 time to fit residues: 104.3340 Evaluate side-chains 244 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 227 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 213 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 ASN B 604 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14946 Z= 0.259 Angle : 0.585 11.700 20288 Z= 0.295 Chirality : 0.041 0.157 2307 Planarity : 0.004 0.053 2493 Dihedral : 5.853 82.955 2059 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.20 % Allowed : 15.89 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1756 helix: 1.10 (0.15), residues: 1147 sheet: -2.53 (0.66), residues: 54 loop : -1.57 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 171 HIS 0.013 0.001 HIS C 242 PHE 0.017 0.001 PHE C 301 TYR 0.027 0.002 TYR C 573 ARG 0.004 0.000 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7962 (mp10) REVERT: A 256 LEU cc_start: 0.9079 (tp) cc_final: 0.8872 (tp) REVERT: A 410 ARG cc_start: 0.7099 (tpm170) cc_final: 0.6678 (tpp-160) REVERT: A 473 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6209 (t-90) REVERT: A 478 LYS cc_start: 0.7467 (ptmt) cc_final: 0.6816 (tppt) REVERT: B 175 ILE cc_start: 0.9027 (tp) cc_final: 0.8657 (tp) REVERT: B 254 LEU cc_start: 0.8827 (tp) cc_final: 0.8536 (tp) REVERT: B 546 TYR cc_start: 0.7569 (p90) cc_final: 0.7280 (p90) REVERT: C 200 LEU cc_start: 0.9143 (tp) cc_final: 0.8886 (tp) REVERT: C 353 ILE cc_start: 0.8655 (mm) cc_final: 0.8328 (mt) REVERT: C 422 GLN cc_start: 0.8738 (tp40) cc_final: 0.8436 (tp40) REVERT: C 462 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8058 (t0) REVERT: C 509 ILE cc_start: 0.8416 (mm) cc_final: 0.8065 (mt) REVERT: C 580 SER cc_start: 0.8123 (OUTLIER) cc_final: 0.7724 (p) REVERT: D 248 ASP cc_start: 0.5634 (t0) cc_final: 0.5191 (t0) REVERT: D 286 ASP cc_start: 0.8400 (p0) cc_final: 0.7944 (p0) REVERT: D 291 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7924 (ttp-170) REVERT: D 342 GLU cc_start: 0.7855 (tt0) cc_final: 0.7622 (tm-30) REVERT: D 352 ARG cc_start: 0.6874 (mpp80) cc_final: 0.6653 (mpp80) outliers start: 35 outliers final: 25 residues processed: 266 average time/residue: 0.2579 time to fit residues: 101.5213 Evaluate side-chains 260 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 537 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.0030 chunk 152 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 chunk 163 optimal weight: 4.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 604 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14946 Z= 0.156 Angle : 0.544 10.744 20288 Z= 0.274 Chirality : 0.039 0.145 2307 Planarity : 0.004 0.057 2493 Dihedral : 5.573 85.705 2059 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.51 % Allowed : 17.46 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1756 helix: 1.39 (0.15), residues: 1142 sheet: -2.48 (0.67), residues: 54 loop : -1.40 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.012 0.001 HIS C 242 PHE 0.024 0.001 PHE C 226 TYR 0.025 0.001 TYR C 573 ARG 0.004 0.000 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7935 (mp10) REVERT: A 410 ARG cc_start: 0.7155 (tpm170) cc_final: 0.6935 (mmm160) REVERT: A 473 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6641 (m170) REVERT: A 478 LYS cc_start: 0.7408 (ptmt) cc_final: 0.6767 (tppt) REVERT: A 508 TYR cc_start: 0.8507 (m-80) cc_final: 0.8294 (m-80) REVERT: A 579 LEU cc_start: 0.7595 (tt) cc_final: 0.7360 (mp) REVERT: B 254 LEU cc_start: 0.8773 (tp) cc_final: 0.8453 (tp) REVERT: B 425 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8465 (tp-100) REVERT: B 464 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7923 (mm) REVERT: B 524 GLU cc_start: 0.7805 (tp30) cc_final: 0.7578 (tp30) REVERT: B 546 TYR cc_start: 0.7526 (p90) cc_final: 0.7267 (p90) REVERT: C 200 LEU cc_start: 0.9092 (tp) cc_final: 0.8855 (tp) REVERT: C 414 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8158 (mp10) REVERT: C 422 GLN cc_start: 0.8670 (tp40) cc_final: 0.8375 (tp40) REVERT: C 462 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8037 (t0) REVERT: C 509 ILE cc_start: 0.8334 (mm) cc_final: 0.7966 (mt) REVERT: C 519 MET cc_start: 0.8666 (ttp) cc_final: 0.8390 (ttt) REVERT: C 580 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7730 (p) REVERT: C 599 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8030 (tp30) REVERT: D 286 ASP cc_start: 0.8409 (p0) cc_final: 0.8153 (p0) REVERT: D 291 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7870 (ttp-170) REVERT: D 342 GLU cc_start: 0.7825 (tt0) cc_final: 0.7617 (tm-30) REVERT: D 352 ARG cc_start: 0.6907 (mpp80) cc_final: 0.6638 (mpp80) REVERT: D 423 GLN cc_start: 0.8379 (tp40) cc_final: 0.7721 (tp40) REVERT: D 534 TYR cc_start: 0.7548 (m-10) cc_final: 0.7316 (m-10) outliers start: 24 outliers final: 16 residues processed: 258 average time/residue: 0.2681 time to fit residues: 102.0415 Evaluate side-chains 251 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 213 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 0.0060 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 0.0370 overall best weight: 0.5874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14946 Z= 0.165 Angle : 0.545 10.657 20288 Z= 0.274 Chirality : 0.039 0.142 2307 Planarity : 0.004 0.056 2493 Dihedral : 5.431 87.073 2059 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.88 % Allowed : 17.78 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1756 helix: 1.44 (0.15), residues: 1148 sheet: -2.70 (0.62), residues: 59 loop : -1.29 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 171 HIS 0.010 0.001 HIS C 242 PHE 0.036 0.001 PHE C 226 TYR 0.023 0.001 TYR C 573 ARG 0.004 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7940 (mp10) REVERT: A 410 ARG cc_start: 0.7123 (tpm170) cc_final: 0.6913 (mmm160) REVERT: A 473 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6098 (t-90) REVERT: A 478 LYS cc_start: 0.7404 (ptmt) cc_final: 0.6754 (tppt) REVERT: A 508 TYR cc_start: 0.8501 (m-80) cc_final: 0.8280 (m-80) REVERT: B 175 ILE cc_start: 0.8983 (tp) cc_final: 0.8585 (tp) REVERT: B 254 LEU cc_start: 0.8832 (tp) cc_final: 0.8478 (tp) REVERT: B 460 LEU cc_start: 0.8559 (mt) cc_final: 0.8327 (pt) REVERT: B 464 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7991 (mm) REVERT: B 546 TYR cc_start: 0.7516 (p90) cc_final: 0.7258 (p90) REVERT: C 200 LEU cc_start: 0.9097 (tp) cc_final: 0.8859 (tp) REVERT: C 422 GLN cc_start: 0.8666 (tp40) cc_final: 0.8364 (tp40) REVERT: C 462 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8053 (t0) REVERT: C 509 ILE cc_start: 0.8335 (mm) cc_final: 0.7980 (mt) REVERT: C 519 MET cc_start: 0.8672 (ttp) cc_final: 0.8383 (ttt) REVERT: C 580 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7725 (p) REVERT: C 599 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7958 (tp30) REVERT: C 607 MET cc_start: 0.6607 (mmm) cc_final: 0.6360 (mmt) REVERT: D 286 ASP cc_start: 0.8320 (p0) cc_final: 0.8075 (p0) REVERT: D 291 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7915 (ttp-170) outliers start: 30 outliers final: 19 residues processed: 260 average time/residue: 0.2520 time to fit residues: 97.7333 Evaluate side-chains 252 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 229 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 435 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 153 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14946 Z= 0.223 Angle : 0.566 10.131 20288 Z= 0.286 Chirality : 0.040 0.151 2307 Planarity : 0.004 0.057 2493 Dihedral : 5.334 88.591 2059 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.57 % Allowed : 18.03 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1756 helix: 1.44 (0.15), residues: 1150 sheet: -2.79 (0.61), residues: 59 loop : -1.27 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.004 0.001 HIS A 473 PHE 0.027 0.001 PHE C 226 TYR 0.022 0.001 TYR C 573 ARG 0.005 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8530 (mm-40) cc_final: 0.7964 (mp10) REVERT: A 410 ARG cc_start: 0.7160 (tpm170) cc_final: 0.6914 (mmm160) REVERT: A 473 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6176 (t-90) REVERT: A 478 LYS cc_start: 0.7372 (ptmt) cc_final: 0.6711 (tppt) REVERT: A 508 TYR cc_start: 0.8494 (m-80) cc_final: 0.8275 (m-80) REVERT: A 579 LEU cc_start: 0.7378 (tt) cc_final: 0.7155 (mp) REVERT: B 175 ILE cc_start: 0.9026 (tp) cc_final: 0.8694 (tp) REVERT: B 254 LEU cc_start: 0.8846 (tp) cc_final: 0.8513 (tp) REVERT: B 425 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8539 (tp-100) REVERT: B 464 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8010 (mm) REVERT: B 546 TYR cc_start: 0.7551 (p90) cc_final: 0.7276 (p90) REVERT: C 200 LEU cc_start: 0.9117 (tp) cc_final: 0.8876 (tp) REVERT: C 414 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8198 (mp10) REVERT: C 422 GLN cc_start: 0.8685 (tp40) cc_final: 0.8381 (tp40) REVERT: C 509 ILE cc_start: 0.8336 (mm) cc_final: 0.7977 (mt) REVERT: C 519 MET cc_start: 0.8645 (ttp) cc_final: 0.8370 (ttt) REVERT: C 580 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7757 (p) REVERT: C 599 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8035 (tp30) REVERT: D 286 ASP cc_start: 0.8292 (p0) cc_final: 0.8058 (p0) REVERT: D 291 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7911 (ttp-170) REVERT: D 534 TYR cc_start: 0.7599 (m-10) cc_final: 0.7381 (m-10) outliers start: 25 outliers final: 16 residues processed: 253 average time/residue: 0.2627 time to fit residues: 98.7209 Evaluate side-chains 245 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 226 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 435 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 157 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14946 Z= 0.166 Angle : 0.543 10.285 20288 Z= 0.274 Chirality : 0.039 0.143 2307 Planarity : 0.004 0.058 2493 Dihedral : 5.211 87.290 2059 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.32 % Allowed : 18.53 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1756 helix: 1.55 (0.15), residues: 1148 sheet: -2.56 (0.66), residues: 54 loop : -1.22 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 171 HIS 0.004 0.001 HIS A 473 PHE 0.024 0.001 PHE C 226 TYR 0.022 0.001 TYR A 423 ARG 0.004 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 231 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7948 (mp10) REVERT: A 410 ARG cc_start: 0.7146 (tpm170) cc_final: 0.6933 (mmm160) REVERT: A 473 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.6172 (t-90) REVERT: A 478 LYS cc_start: 0.7356 (ptmt) cc_final: 0.7150 (mmmt) REVERT: A 508 TYR cc_start: 0.8464 (m-80) cc_final: 0.8238 (m-80) REVERT: B 254 LEU cc_start: 0.8843 (tp) cc_final: 0.8515 (tp) REVERT: B 425 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8510 (tp-100) REVERT: B 464 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 546 TYR cc_start: 0.7511 (p90) cc_final: 0.7253 (p90) REVERT: C 200 LEU cc_start: 0.9100 (tp) cc_final: 0.8857 (tp) REVERT: C 414 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8134 (mp10) REVERT: C 422 GLN cc_start: 0.8679 (tp40) cc_final: 0.8390 (tp40) REVERT: C 509 ILE cc_start: 0.8390 (mm) cc_final: 0.8054 (mt) REVERT: C 519 MET cc_start: 0.8625 (ttp) cc_final: 0.8397 (ttt) REVERT: C 580 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7723 (p) REVERT: C 599 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8030 (tp30) REVERT: D 286 ASP cc_start: 0.8237 (p0) cc_final: 0.8025 (p0) REVERT: D 291 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7912 (ttp-170) REVERT: D 423 GLN cc_start: 0.8415 (tp40) cc_final: 0.7807 (tp40) REVERT: D 534 TYR cc_start: 0.7605 (m-10) cc_final: 0.7402 (m-10) outliers start: 21 outliers final: 14 residues processed: 247 average time/residue: 0.2612 time to fit residues: 95.7730 Evaluate side-chains 243 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 604 GLN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 0.0370 chunk 115 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 14946 Z= 0.250 Angle : 0.753 59.191 20288 Z= 0.425 Chirality : 0.040 0.344 2307 Planarity : 0.004 0.061 2493 Dihedral : 5.207 87.308 2059 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.13 % Allowed : 19.10 % Favored : 79.77 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1756 helix: 1.54 (0.15), residues: 1148 sheet: -2.56 (0.66), residues: 54 loop : -1.21 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 171 HIS 0.005 0.001 HIS C 242 PHE 0.025 0.001 PHE D 310 TYR 0.056 0.001 TYR B 591 ARG 0.003 0.000 ARG B 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8512 (mm-40) cc_final: 0.7948 (mp10) REVERT: A 410 ARG cc_start: 0.7169 (tpm170) cc_final: 0.6914 (mmm160) REVERT: A 473 HIS cc_start: 0.6771 (OUTLIER) cc_final: 0.6172 (t-90) REVERT: A 478 LYS cc_start: 0.7382 (ptmt) cc_final: 0.7150 (mmmt) REVERT: A 508 TYR cc_start: 0.8460 (m-80) cc_final: 0.8241 (m-80) REVERT: B 254 LEU cc_start: 0.8844 (tp) cc_final: 0.8515 (tp) REVERT: B 424 MET cc_start: 0.8502 (mtm) cc_final: 0.8288 (mtp) REVERT: B 425 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8502 (tp-100) REVERT: B 464 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7987 (mm) REVERT: B 546 TYR cc_start: 0.7511 (p90) cc_final: 0.7253 (p90) REVERT: C 200 LEU cc_start: 0.9100 (tp) cc_final: 0.8858 (tp) REVERT: C 414 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8134 (mp10) REVERT: C 422 GLN cc_start: 0.8681 (tp40) cc_final: 0.8391 (tp40) REVERT: C 509 ILE cc_start: 0.8391 (mm) cc_final: 0.8045 (mt) REVERT: C 519 MET cc_start: 0.8627 (ttp) cc_final: 0.8399 (ttt) REVERT: C 580 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7724 (p) REVERT: C 599 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8028 (tp30) REVERT: D 286 ASP cc_start: 0.8238 (p0) cc_final: 0.8028 (p0) REVERT: D 291 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7911 (ttp-170) REVERT: D 423 GLN cc_start: 0.8417 (tp40) cc_final: 0.7810 (tp40) outliers start: 18 outliers final: 14 residues processed: 240 average time/residue: 0.2617 time to fit residues: 93.8922 Evaluate side-chains 242 residues out of total 1588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137596 restraints weight = 25611.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133647 restraints weight = 30470.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131247 restraints weight = 28152.406| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 14946 Z= 0.250 Angle : 0.753 59.191 20288 Z= 0.425 Chirality : 0.040 0.344 2307 Planarity : 0.004 0.063 2493 Dihedral : 5.207 87.308 2059 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.07 % Allowed : 19.22 % Favored : 79.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1756 helix: 1.54 (0.15), residues: 1148 sheet: -2.56 (0.66), residues: 54 loop : -1.21 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 171 HIS 0.005 0.001 HIS C 242 PHE 0.025 0.001 PHE D 310 TYR 0.056 0.001 TYR B 591 ARG 0.003 0.000 ARG B 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.89 seconds wall clock time: 57 minutes 21.56 seconds (3441.56 seconds total)