Starting phenix.real_space_refine on Sat Mar 16 11:09:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evc_28626/03_2024/8evc_28626_neut_updated.pdb" } resolution = 3.33 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= 0.001 sd= 0.034 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 65 5.16 5 C 9470 2.51 5 N 2369 2.21 5 O 2623 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 189": "NH1" <-> "NH2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 455": "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 GLU 524": "OE1" <-> "OE2" Residue "B ASP 532": "OD1" <-> "OD2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C ASP 211": "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 PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" 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 376": "OE1" <-> "OE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C ASP 532": "OD1" <-> "OD2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ASP 575": "OD1" <-> "OD2" Residue "C GLU 593": "OE1" <-> "OE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 342": "OE1" <-> "OE2" 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 TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 535": "OD1" <-> "OD2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D ASP 576": "OD1" <-> "OD2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 620": "OD1" <-> "OD2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14531 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3632 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 14, 'TRANS': 431} Chain breaks: 1 Chain: "B" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3565 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 13, 'TRANS': 422} Chain breaks: 2 Chain: "C" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3598 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain breaks: 1 Chain: "D" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} 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: 7.02, per 1000 atoms: 0.48 Number of scatterers: 14531 At special positions: 0 Unit cell: (104.58, 108.73, 124.5, 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 65 16.00 P 4 15.00 O 2623 8.00 N 2369 7.00 C 9470 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: 5.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 10 sheets defined 58.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 167 through 191 Proline residue: A 178 - end of helix removed outlier: 5.453A pdb=" N ILE A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.739A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 197' Processing helix chain 'A' and resid 201 through 223 removed outlier: 3.970A pdb=" N ARG A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 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: 4.099A pdb=" N MET A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' 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 552 No H-bonds generated for 'chain 'A' and resid 549 through 552' Processing helix chain 'A' and resid 581 through 587 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 274 through 279 removed outlier: 3.720A 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 409 through 426 Processing helix chain 'B' and resid 431 through 446 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 479 removed outlier: 5.756A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 removed outlier: 4.243A pdb=" N LEU B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 497' Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 592 through 609 Processing helix chain 'C' and resid 166 through 189 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 200 through 222 Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 282 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 426 removed outlier: 5.240A pdb=" N SER C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 462 through 478 removed outlier: 5.107A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 496 Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 593 through 606 Processing helix chain 'D' and resid 216 through 241 removed outlier: 3.522A pdb=" N ALA D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 250 through 274 Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 311 through 317 removed outlier: 4.163A pdb=" N LEU D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 316 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 Processing helix chain 'D' and resid 348 through 378 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.805A pdb=" N TRP D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) 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 489 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 504 through 521 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 597 through 599 No H-bonds generated for 'chain 'D' and resid 597 through 599' Processing helix chain 'D' and resid 621 through 630 removed outlier: 4.526A 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 499 through 503 Processing sheet with id= B, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.950A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 568 " --> pdb=" O CYS A 510 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS A 510 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER A 570 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A 508 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 499 through 503 Processing sheet with id= D, first strand: chain 'B' and resid 527 through 529 Processing sheet with id= E, first strand: chain 'C' and resid 501 through 503 Processing sheet with id= F, first strand: chain 'C' and resid 527 through 530 removed outlier: 3.920A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.014A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 541 through 545 Processing sheet with id= I, first strand: chain 'D' and resid 562 through 564 removed outlier: 3.555A pdb=" N SER D 588 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 569 through 572 770 hydrogen bonds defined for protein. 2274 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: 4.09 Time building geometry restraints manager: 5.97 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: 4302 1.34 - 1.46: 3330 1.46 - 1.58: 7142 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 14878 Sorted by residual: bond pdb=" C2' PCG A 802 " pdb=" C3' PCG A 802 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+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=" C2' PCG B 802 " pdb=" C3' PCG B 802 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C2' PCG C 802 " pdb=" C3' PCG C 802 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.38e+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 14873 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.94: 294 105.94 - 113.93: 8410 113.93 - 121.92: 8786 121.92 - 129.91: 2602 129.91 - 137.90: 102 Bond angle restraints: 20194 Sorted by residual: angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 112.23 128.13 -15.90 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 112.23 128.12 -15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 128.11 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 112.23 128.07 -15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C2 PCG A 802 " pdb=" N3 PCG A 802 " pdb=" C4 PCG A 802 " ideal model delta sigma weight residual 120.18 106.86 13.32 3.00e+00 1.11e-01 1.97e+01 ... (remaining 20189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7869 17.98 - 35.96: 789 35.96 - 53.95: 119 53.95 - 71.93: 24 71.93 - 89.91: 17 Dihedral angle restraints: 8818 sinusoidal: 3621 harmonic: 5197 Sorted by residual: dihedral pdb=" CA THR A 245 " pdb=" C THR A 245 " pdb=" N THR A 246 " pdb=" CA THR A 246 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" N SER C 558 " pdb=" C SER C 558 " pdb=" CA SER C 558 " pdb=" CB SER C 558 " ideal model delta harmonic sigma weight residual 122.80 135.17 -12.37 0 2.50e+00 1.60e-01 2.45e+01 dihedral pdb=" C THR B 536 " pdb=" N THR B 536 " pdb=" CA THR B 536 " pdb=" CB THR B 536 " ideal model delta harmonic sigma weight residual -122.00 -133.71 11.71 0 2.50e+00 1.60e-01 2.20e+01 ... (remaining 8815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2281 0.336 - 0.672: 12 0.672 - 1.008: 0 1.008 - 1.345: 0 1.345 - 1.681: 4 Chirality restraints: 2297 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 -0.72 -1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.06e+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 -0.72 -1.68 2.00e-01 2.50e+01 7.03e+01 ... (remaining 2294 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 389 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C VAL A 389 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL A 389 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 390 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 512 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C ILE D 512 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE D 512 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP D 513 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 268 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C MET D 268 " 0.052 2.00e-02 2.50e+03 pdb=" O MET D 268 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU D 269 " -0.018 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2077 2.76 - 3.30: 13587 3.30 - 3.83: 24787 3.83 - 4.37: 27726 4.37 - 4.90: 48277 Nonbonded interactions: 116454 Sorted by model distance: nonbonded pdb=" NZ LYS B 512 " pdb=" O THR B 565 " model vdw 2.228 2.520 nonbonded pdb=" O THR C 360 " pdb=" OG1 THR C 364 " model vdw 2.267 2.440 nonbonded pdb=" NH1 ARG B 564 " pdb=" O2A PCG B 802 " model vdw 2.304 2.520 nonbonded pdb=" OG1 THR A 476 " pdb=" OD1 ASN A 523 " model vdw 2.306 2.440 nonbonded pdb=" O TYR D 294 " pdb=" OG SER D 297 " model vdw 2.331 2.440 ... (remaining 116449 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 257 or resid 269 through 483 or resid 489 thro \ ugh 607 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 607 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 257 or resid 269 through 483 or resid 489 thro \ ugh 607 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.020 Extract box with map and model: 7.100 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 38.810 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.013 0.368 14878 Z= 0.853 Angle : 1.090 15.901 20194 Z= 0.542 Chirality : 0.098 1.681 2297 Planarity : 0.008 0.069 2480 Dihedral : 14.648 89.911 5478 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.95 % Allowed : 4.29 % Favored : 94.76 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.14), residues: 1748 helix: -2.78 (0.10), residues: 1115 sheet: -2.84 (0.48), residues: 74 loop : -2.49 (0.22), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 240 HIS 0.007 0.002 HIS B 473 PHE 0.043 0.002 PHE D 427 TYR 0.039 0.002 TYR D 314 ARG 0.015 0.001 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 238 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8563 (tp) cc_final: 0.8358 (tp) REVERT: B 175 ILE cc_start: 0.8695 (tp) cc_final: 0.8349 (tp) REVERT: B 445 TRP cc_start: 0.8669 (t-100) cc_final: 0.8377 (t-100) REVERT: B 526 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7898 (mmtm) REVERT: C 184 TYR cc_start: 0.7581 (m-80) cc_final: 0.7080 (m-80) REVERT: C 407 ASN cc_start: 0.7542 (t0) cc_final: 0.6957 (t0) REVERT: D 532 MET cc_start: 0.4701 (tmm) cc_final: 0.4458 (tmm) REVERT: D 608 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7235 (p) REVERT: D 639 MET cc_start: 0.6085 (mmp) cc_final: 0.4718 (mtt) outliers start: 15 outliers final: 3 residues processed: 253 average time/residue: 0.2827 time to fit residues: 102.3711 Evaluate side-chains 158 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN C 182 ASN C 229 GLN C 414 GLN C 425 GLN D 276 GLN D 340 HIS D 367 ASN D 426 ASN D 468 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14878 Z= 0.163 Angle : 0.511 8.009 20194 Z= 0.269 Chirality : 0.039 0.256 2297 Planarity : 0.005 0.047 2480 Dihedral : 5.253 46.279 2056 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.20 % Allowed : 9.53 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.18), residues: 1748 helix: -0.53 (0.14), residues: 1111 sheet: -2.46 (0.54), residues: 68 loop : -2.00 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 171 HIS 0.003 0.001 HIS C 315 PHE 0.014 0.001 PHE C 180 TYR 0.015 0.001 TYR D 387 ARG 0.008 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.638 Fit side-chains REVERT: A 175 ILE cc_start: 0.8454 (tp) cc_final: 0.8254 (tp) REVERT: A 421 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7535 (mtmt) REVERT: B 518 GLU cc_start: 0.7857 (pt0) cc_final: 0.7646 (pt0) REVERT: B 526 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7732 (mmtm) REVERT: B 585 MET cc_start: 0.7545 (mmm) cc_final: 0.7303 (tpp) REVERT: C 184 TYR cc_start: 0.7568 (m-80) cc_final: 0.7073 (m-80) REVERT: C 274 ARG cc_start: 0.7003 (mmt-90) cc_final: 0.6695 (mpt180) REVERT: C 604 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: D 322 MET cc_start: 0.5965 (ttt) cc_final: 0.5073 (tmm) REVERT: D 532 MET cc_start: 0.4440 (tmm) cc_final: 0.4181 (ppp) outliers start: 19 outliers final: 9 residues processed: 194 average time/residue: 0.2342 time to fit residues: 70.0068 Evaluate side-chains 166 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 159 optimal weight: 0.0470 chunk 171 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN B 345 HIS B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 272 GLN D 276 GLN D 423 GLN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14878 Z= 0.310 Angle : 0.570 7.350 20194 Z= 0.298 Chirality : 0.042 0.229 2297 Planarity : 0.004 0.050 2480 Dihedral : 5.033 53.879 2055 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.59 % Allowed : 11.62 % Favored : 85.80 % 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: -0.78 (0.19), residues: 1748 helix: 0.29 (0.15), residues: 1101 sheet: -1.97 (0.52), residues: 88 loop : -1.79 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 171 HIS 0.004 0.001 HIS D 365 PHE 0.020 0.002 PHE C 392 TYR 0.015 0.002 TYR B 354 ARG 0.005 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 1.707 Fit side-chains REVERT: A 175 ILE cc_start: 0.8673 (tp) cc_final: 0.8473 (tp) REVERT: A 427 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6987 (mtt180) REVERT: B 199 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7207 (p90) REVERT: B 425 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 184 TYR cc_start: 0.7650 (m-80) cc_final: 0.7218 (m-80) REVERT: C 274 ARG cc_start: 0.7202 (mmt-90) cc_final: 0.6838 (mpt180) REVERT: C 546 TYR cc_start: 0.7404 (p90) cc_final: 0.7058 (p90) REVERT: D 322 MET cc_start: 0.6082 (ttt) cc_final: 0.5264 (tmm) outliers start: 41 outliers final: 24 residues processed: 188 average time/residue: 0.2277 time to fit residues: 67.0793 Evaluate side-chains 179 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 0.0010 chunk 17 optimal weight: 0.0970 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 272 GLN D 276 GLN ** 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: 0.8090 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 14878 Z= 0.157 Angle : 0.472 7.879 20194 Z= 0.247 Chirality : 0.039 0.186 2297 Planarity : 0.003 0.039 2480 Dihedral : 4.656 52.185 2055 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.08 % Allowed : 13.83 % Favored : 84.09 % 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: -0.04 (0.20), residues: 1748 helix: 0.92 (0.16), residues: 1101 sheet: -2.34 (0.50), residues: 83 loop : -1.49 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.002 0.001 HIS D 251 PHE 0.015 0.001 PHE C 180 TYR 0.009 0.001 TYR A 297 ARG 0.003 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.690 Fit side-chains REVERT: A 493 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6164 (tm-30) REVERT: A 607 MET cc_start: 0.7700 (mmp) cc_final: 0.7458 (mmp) REVERT: B 175 ILE cc_start: 0.8687 (tp) cc_final: 0.8351 (tp) REVERT: B 241 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7653 (mt0) REVERT: C 184 TYR cc_start: 0.7498 (m-80) cc_final: 0.7051 (m-80) REVERT: C 274 ARG cc_start: 0.7050 (mmt-90) cc_final: 0.6780 (mpt180) REVERT: C 407 ASN cc_start: 0.7691 (t0) cc_final: 0.7457 (t0) REVERT: C 546 TYR cc_start: 0.7357 (p90) cc_final: 0.6993 (p90) REVERT: C 604 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: D 322 MET cc_start: 0.5981 (ttt) cc_final: 0.5245 (tmm) REVERT: D 639 MET cc_start: 0.6150 (mmp) cc_final: 0.4590 (mtt) outliers start: 33 outliers final: 19 residues processed: 196 average time/residue: 0.2326 time to fit residues: 70.2889 Evaluate side-chains 179 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.0000 chunk 144 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN C 425 GLN D 272 GLN D 276 GLN ** 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: 0.8125 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14878 Z= 0.213 Angle : 0.499 7.989 20194 Z= 0.259 Chirality : 0.040 0.168 2297 Planarity : 0.003 0.038 2480 Dihedral : 4.250 27.810 2049 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.40 % Allowed : 14.65 % Favored : 82.95 % 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: 0.19 (0.20), residues: 1748 helix: 1.10 (0.16), residues: 1100 sheet: -2.17 (0.53), residues: 77 loop : -1.42 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.004 0.001 HIS C 473 PHE 0.014 0.001 PHE C 180 TYR 0.018 0.001 TYR B 297 ARG 0.003 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.625 Fit side-chains REVERT: A 427 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6765 (mtt180) REVERT: A 493 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: A 524 GLU cc_start: 0.7860 (tt0) cc_final: 0.7417 (tm-30) REVERT: B 241 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7691 (mt0) REVERT: B 407 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7386 (p0) REVERT: B 514 ASP cc_start: 0.8052 (t0) cc_final: 0.7659 (t0) REVERT: C 184 TYR cc_start: 0.7572 (m-80) cc_final: 0.7126 (m-80) REVERT: C 274 ARG cc_start: 0.7143 (mmt-90) cc_final: 0.6857 (mpt180) REVERT: C 384 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8579 (t0) REVERT: C 546 TYR cc_start: 0.7456 (p90) cc_final: 0.6985 (p90) REVERT: C 604 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: D 322 MET cc_start: 0.6086 (ttt) cc_final: 0.5327 (tmm) outliers start: 38 outliers final: 26 residues processed: 196 average time/residue: 0.2304 time to fit residues: 69.5785 Evaluate side-chains 189 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 425 GLN D 272 GLN D 276 GLN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 14878 Z= 0.176 Angle : 0.479 8.660 20194 Z= 0.250 Chirality : 0.039 0.178 2297 Planarity : 0.003 0.034 2480 Dihedral : 4.150 27.579 2049 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.65 % Allowed : 14.71 % Favored : 82.64 % 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: 0.39 (0.20), residues: 1748 helix: 1.25 (0.16), residues: 1105 sheet: -2.10 (0.54), residues: 77 loop : -1.35 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.003 0.001 HIS C 473 PHE 0.014 0.001 PHE C 180 TYR 0.016 0.001 TYR D 377 ARG 0.004 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.668 Fit side-chains REVERT: A 427 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6760 (mtt180) REVERT: A 493 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6144 (tm-30) REVERT: A 524 GLU cc_start: 0.7862 (tt0) cc_final: 0.7413 (tm-30) REVERT: B 241 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7665 (mt0) REVERT: B 407 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7627 (p0) REVERT: C 184 TYR cc_start: 0.7524 (m-80) cc_final: 0.7087 (m-80) REVERT: C 274 ARG cc_start: 0.7123 (mmt-90) cc_final: 0.6822 (mpt180) REVERT: C 546 TYR cc_start: 0.7430 (p90) cc_final: 0.7049 (p90) REVERT: C 604 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: D 322 MET cc_start: 0.6050 (ttt) cc_final: 0.5312 (tmm) outliers start: 42 outliers final: 28 residues processed: 195 average time/residue: 0.2160 time to fit residues: 65.8575 Evaluate side-chains 188 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 272 GLN ** 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: 0.8129 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14878 Z= 0.222 Angle : 0.495 6.474 20194 Z= 0.260 Chirality : 0.040 0.170 2297 Planarity : 0.003 0.033 2480 Dihedral : 4.160 27.803 2049 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.78 % Allowed : 14.52 % Favored : 82.70 % 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: 0.43 (0.20), residues: 1748 helix: 1.29 (0.16), residues: 1103 sheet: -2.12 (0.54), residues: 77 loop : -1.32 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.003 0.001 HIS D 365 PHE 0.014 0.001 PHE C 180 TYR 0.018 0.001 TYR B 297 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 1.744 Fit side-chains REVERT: A 219 LEU cc_start: 0.8506 (mp) cc_final: 0.8161 (tt) REVERT: A 427 ARG cc_start: 0.7158 (mtt180) cc_final: 0.6905 (mtt180) REVERT: A 493 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6152 (tm-30) REVERT: A 524 GLU cc_start: 0.7863 (tt0) cc_final: 0.7385 (tm-30) REVERT: B 241 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7667 (mt0) REVERT: B 407 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7375 (p0) REVERT: B 514 ASP cc_start: 0.8022 (t0) cc_final: 0.7633 (t0) REVERT: B 585 MET cc_start: 0.7781 (mmm) cc_final: 0.7349 (tpp) REVERT: C 184 TYR cc_start: 0.7558 (m-80) cc_final: 0.7102 (m-80) REVERT: C 274 ARG cc_start: 0.7110 (mmt-90) cc_final: 0.6787 (mpt180) REVERT: C 384 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8579 (t0) REVERT: C 414 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8058 (tp40) REVERT: C 546 TYR cc_start: 0.7511 (p90) cc_final: 0.7117 (p90) REVERT: C 604 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: D 322 MET cc_start: 0.6083 (ttt) cc_final: 0.5335 (tmm) REVERT: D 492 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8270 (ptp) REVERT: D 626 GLU cc_start: 0.7646 (pp20) cc_final: 0.7211 (pp20) outliers start: 44 outliers final: 32 residues processed: 196 average time/residue: 0.2266 time to fit residues: 68.8286 Evaluate side-chains 194 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL 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: 4.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14878 Z= 0.234 Angle : 0.506 6.681 20194 Z= 0.265 Chirality : 0.040 0.157 2297 Planarity : 0.003 0.033 2480 Dihedral : 4.179 27.964 2049 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.97 % Allowed : 15.03 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1748 helix: 1.31 (0.16), residues: 1102 sheet: -1.91 (0.54), residues: 82 loop : -1.28 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.003 0.001 HIS D 365 PHE 0.015 0.001 PHE C 180 TYR 0.019 0.001 TYR D 331 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 1.513 Fit side-chains REVERT: A 219 LEU cc_start: 0.8447 (mp) cc_final: 0.8166 (tt) REVERT: A 232 MET cc_start: 0.8271 (ttm) cc_final: 0.7923 (tpp) REVERT: A 427 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6949 (mtt180) REVERT: A 493 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6228 (tm-30) REVERT: A 524 GLU cc_start: 0.7900 (tt0) cc_final: 0.7391 (tm-30) REVERT: B 407 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7235 (p0) REVERT: B 514 ASP cc_start: 0.7991 (t0) cc_final: 0.7605 (t0) REVERT: B 585 MET cc_start: 0.7833 (mmm) cc_final: 0.7446 (tpp) REVERT: C 184 TYR cc_start: 0.7558 (m-80) cc_final: 0.7160 (m-80) REVERT: C 274 ARG cc_start: 0.7152 (mmt-90) cc_final: 0.6805 (mpt180) REVERT: C 342 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7956 (tp) REVERT: C 384 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8583 (t0) REVERT: C 414 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7998 (tp40) REVERT: C 546 TYR cc_start: 0.7538 (p90) cc_final: 0.7046 (p90) REVERT: C 604 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: D 322 MET cc_start: 0.6094 (ttt) cc_final: 0.5338 (tmm) REVERT: D 492 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8277 (ptp) outliers start: 47 outliers final: 34 residues processed: 193 average time/residue: 0.2260 time to fit residues: 68.0017 Evaluate side-chains 197 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14878 Z= 0.213 Angle : 0.502 7.755 20194 Z= 0.262 Chirality : 0.040 0.150 2297 Planarity : 0.003 0.032 2480 Dihedral : 4.145 28.080 2049 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.97 % Allowed : 15.15 % Favored : 81.88 % 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: 0.58 (0.20), residues: 1748 helix: 1.39 (0.16), residues: 1101 sheet: -2.01 (0.52), residues: 87 loop : -1.20 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.003 0.001 HIS D 365 PHE 0.015 0.001 PHE C 180 TYR 0.020 0.001 TYR D 331 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 1.517 Fit side-chains REVERT: A 219 LEU cc_start: 0.8422 (mp) cc_final: 0.8163 (tt) REVERT: A 232 MET cc_start: 0.8253 (ttm) cc_final: 0.7962 (tpp) REVERT: A 427 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6948 (mtt180) REVERT: A 493 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6189 (tm-30) REVERT: A 524 GLU cc_start: 0.7898 (tt0) cc_final: 0.7379 (tm-30) REVERT: B 241 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7597 (mt0) REVERT: B 300 MET cc_start: 0.7043 (mmt) cc_final: 0.6823 (mmt) REVERT: B 407 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7269 (p0) REVERT: B 514 ASP cc_start: 0.8000 (t0) cc_final: 0.7617 (t0) REVERT: B 585 MET cc_start: 0.7805 (mmm) cc_final: 0.7441 (tpp) REVERT: C 184 TYR cc_start: 0.7543 (m-80) cc_final: 0.7142 (m-80) REVERT: C 274 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.6805 (mpt180) REVERT: C 342 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7949 (tp) REVERT: C 384 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8588 (t0) REVERT: C 414 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7964 (tp40) REVERT: C 546 TYR cc_start: 0.7530 (p90) cc_final: 0.7043 (p90) REVERT: C 604 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: D 322 MET cc_start: 0.6116 (ttt) cc_final: 0.5372 (tmm) REVERT: D 492 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8241 (ptp) outliers start: 47 outliers final: 36 residues processed: 193 average time/residue: 0.2230 time to fit residues: 66.9006 Evaluate side-chains 199 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 115 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 14878 Z= 0.172 Angle : 0.481 8.817 20194 Z= 0.251 Chirality : 0.039 0.156 2297 Planarity : 0.003 0.031 2480 Dihedral : 4.046 27.932 2049 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.59 % Allowed : 15.78 % Favored : 81.63 % 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: 0.76 (0.21), residues: 1748 helix: 1.53 (0.16), residues: 1102 sheet: -1.99 (0.55), residues: 77 loop : -1.17 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 171 HIS 0.002 0.001 HIS D 251 PHE 0.014 0.001 PHE C 180 TYR 0.018 0.001 TYR D 331 ARG 0.003 0.000 ARG A 569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.755 Fit side-chains REVERT: A 219 LEU cc_start: 0.8384 (mp) cc_final: 0.8130 (tt) REVERT: A 232 MET cc_start: 0.8219 (ttm) cc_final: 0.7953 (tpp) REVERT: A 427 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6832 (mtt180) REVERT: A 493 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6190 (tm-30) REVERT: A 524 GLU cc_start: 0.7861 (tt0) cc_final: 0.7349 (tm-30) REVERT: B 241 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7572 (mt0) REVERT: B 407 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7282 (p0) REVERT: B 514 ASP cc_start: 0.7993 (t0) cc_final: 0.7618 (t0) REVERT: B 585 MET cc_start: 0.7793 (mmm) cc_final: 0.7472 (tpp) REVERT: C 184 TYR cc_start: 0.7490 (m-80) cc_final: 0.7101 (m-80) REVERT: C 274 ARG cc_start: 0.7149 (mmt-90) cc_final: 0.6815 (mpt180) REVERT: C 384 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8592 (t0) REVERT: C 414 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7942 (tp40) REVERT: C 546 TYR cc_start: 0.7491 (p90) cc_final: 0.7035 (p90) REVERT: C 604 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: D 322 MET cc_start: 0.6085 (ttt) cc_final: 0.5363 (tmm) outliers start: 41 outliers final: 32 residues processed: 196 average time/residue: 0.2248 time to fit residues: 68.4669 Evaluate side-chains 196 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.158040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119830 restraints weight = 19175.132| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.88 r_work: 0.3359 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14878 Z= 0.187 Angle : 0.488 8.919 20194 Z= 0.253 Chirality : 0.039 0.152 2297 Planarity : 0.003 0.032 2480 Dihedral : 4.035 27.880 2049 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.34 % Allowed : 15.97 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1748 helix: 1.54 (0.16), residues: 1101 sheet: -1.81 (0.54), residues: 82 loop : -1.18 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.002 0.001 HIS C 473 PHE 0.014 0.001 PHE C 180 TYR 0.018 0.001 TYR D 331 ARG 0.003 0.000 ARG A 569 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.69 seconds wall clock time: 55 minutes 59.71 seconds (3359.71 seconds total)