Starting phenix.real_space_refine on Fri Feb 16 08:03:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etp_28595/02_2024/8etp_28595_neut_updated.pdb" } resolution = 3.52 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= 0.077 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 9652 2.51 5 N 2410 2.21 5 O 2677 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 GLU 198": "OE1" <-> "OE2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 228": "OE1" <-> "OE2" 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 PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A ASP 532": "OD1" <-> "OD2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 603": "NH1" <-> "NH2" 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 ASP 211": "OD1" <-> "OD2" 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 PHE 281": "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 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 455": "OE1" <-> "OE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" 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 TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B ASP 532": "OD1" <-> "OD2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ASP 207": "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 ARG 410": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C PHE 538": "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 TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 582": "OD1" <-> "OD2" Residue "C GLU 590": "OE1" <-> "OE2" 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 "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 257": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" 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 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 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 ASP 388": "OD1" <-> "OD2" Residue "D GLU 390": "OE1" <-> "OE2" 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 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ASP 461": "OD1" <-> "OD2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 494": "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 GLU 592": "OE1" <-> "OE2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D ASP 620": "OD1" <-> "OD2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14809 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3684 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Conformer: "B" Number of residues, atoms: 452, 3684 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} bond proxies already assigned to first conformer: 3758 Chain: "B" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3684 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3697 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} 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: 9.53, per 1000 atoms: 0.64 Number of scatterers: 14809 At special positions: 0 Unit cell: (132.25, 118.496, 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 2677 8.00 N 2410 7.00 C 9652 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: 5.37 Conformation dependent library (CDL) restraints added in 3.3 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 9 sheets defined 59.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 166 through 192 Proline residue: A 178 - end of helix 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 255 Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.561A pdb=" N VAL A 266 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 removed outlier: 4.280A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (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 406 Processing helix chain 'A' and resid 408 through 426 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 470 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 496 Processing helix chain 'A' and resid 550 through 553 No H-bonds generated for 'chain 'A' and resid 550 through 553' 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 260 through 266 removed outlier: 4.062A pdb=" N LEU B 264 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 266 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 removed outlier: 4.533A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 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 426 removed outlier: 5.280A pdb=" N SER B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG B 410 " --> pdb=" O MET B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.842A pdb=" N LYS B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 477 removed outlier: 5.979A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 483 No H-bonds generated for 'chain 'B' and resid 481 through 483' Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 592 through 609 Processing helix chain 'C' and resid 166 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 247 through 255 Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 273 through 279 removed outlier: 4.214A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 279 " --> pdb=" O ASN C 276 " (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 426 removed outlier: 5.701A pdb=" N SER C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 5.595A 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 453 through 456 No H-bonds generated for 'chain 'C' and resid 453 through 456' Processing helix chain 'C' and resid 462 through 477 removed outlier: 6.114A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 592 through 609 Processing helix chain 'D' and resid 216 through 241 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 250 through 270 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 299 through 306 Processing helix chain 'D' and resid 310 through 317 removed outlier: 4.249A pdb=" N PHE D 317 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 329 removed outlier: 4.311A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET D 328 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 Processing helix chain 'D' and resid 348 through 377 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 489 Processing helix chain 'D' and resid 496 through 501 removed outlier: 4.339A pdb=" N THR D 501 " --> pdb=" O ASP D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 520 removed outlier: 3.856A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 592 through 595 removed outlier: 3.634A pdb=" N LEU D 595 " --> pdb=" O GLU D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 621 through 628 Processing helix chain 'D' and resid 632 through 645 Processing sheet with id= A, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.768A pdb=" N ASP A 575 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.566A pdb=" N ALA A 528 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 500 through 503 removed outlier: 3.558A pdb=" N ILE B 521 " --> pdb=" O PHE B 577 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 567 through 570 removed outlier: 3.904A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 539 " --> pdb=" O VAL B 529 " (cutoff:3.500A) 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 567 through 570 removed outlier: 3.605A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 529 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 539 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.481A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 279 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 560 through 565 removed outlier: 3.511A pdb=" N ASN D 615 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 569 through 572 removed outlier: 3.773A pdb=" N ASN D 607 " --> pdb=" O LEU D 572 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2315 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: 4.23 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2339 1.31 - 1.44: 4238 1.44 - 1.56: 8474 1.56 - 1.69: 10 1.69 - 1.82: 105 Bond restraints: 15166 Sorted by residual: 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 3.41e+02 bond pdb=" C2' PCG D 901 " pdb=" C3' PCG D 901 " 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 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 3.40e+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 3.39e+02 bond pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " ideal model delta sigma weight residual 1.808 1.532 0.276 2.00e-02 2.50e+03 1.90e+02 ... (remaining 15161 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.82: 289 105.82 - 113.84: 8467 113.84 - 121.86: 8929 121.86 - 129.88: 2807 129.88 - 137.90: 102 Bond angle restraints: 20594 Sorted by residual: angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 112.23 128.22 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 112.23 128.05 -15.82 3.00e+00 1.11e-01 2.78e+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 C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 127.84 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" N ALA A 566 " pdb=" CA ALA A 566 " pdb=" C ALA A 566 " ideal model delta sigma weight residual 110.80 121.73 -10.93 2.13e+00 2.20e-01 2.63e+01 ... (remaining 20589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.32: 7971 18.32 - 36.64: 858 36.64 - 54.96: 135 54.96 - 73.29: 18 73.29 - 91.61: 13 Dihedral angle restraints: 8995 sinusoidal: 3686 harmonic: 5309 Sorted by residual: dihedral pdb=" C ALA A 566 " pdb=" N ALA A 566 " pdb=" CA ALA A 566 " pdb=" CB ALA A 566 " ideal model delta harmonic sigma weight residual -122.60 -134.31 11.71 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" N ALA A 566 " pdb=" C ALA A 566 " pdb=" CA ALA A 566 " pdb=" CB ALA A 566 " ideal model delta harmonic sigma weight residual 122.90 134.59 -11.69 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" CA ASN C 447 " pdb=" C ASN C 447 " pdb=" N LYS C 448 " pdb=" CA LYS C 448 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 2329 0.333 - 0.665: 7 0.665 - 0.998: 3 0.998 - 1.331: 0 1.331 - 1.664: 4 Chirality restraints: 2343 Sorted by residual: 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 -0.73 -1.66 2.00e-01 2.50e+01 6.92e+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 -0.74 -1.66 2.00e-01 2.50e+01 6.89e+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 -0.81 -1.58 2.00e-01 2.50e+01 6.27e+01 ... (remaining 2340 not shown) Planarity restraints: 2536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 562 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ASN A 562 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 562 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG A 563 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.73e+00 pdb=" N PRO D 273 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 504 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO C 505 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 505 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 505 " -0.038 5.00e-02 4.00e+02 ... (remaining 2533 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4938 2.85 - 3.36: 13379 3.36 - 3.87: 25208 3.87 - 4.39: 27497 4.39 - 4.90: 47483 Nonbonded interactions: 118505 Sorted by model distance: nonbonded pdb=" OG SER C 504 " pdb=" OD1 ASP C 507 " model vdw 2.332 2.440 nonbonded pdb=" O PHE D 516 " pdb=" OG SER D 520 " model vdw 2.339 2.440 nonbonded pdb=" O ALA B 415 " pdb=" OG SER B 419 " model vdw 2.342 2.440 nonbonded pdb=" OG1 THR A 430 " pdb=" OD1 ASP A 432 " model vdw 2.370 2.440 nonbonded pdb=" OE1 GLU D 560 " pdb=" OH TYR D 562 " model vdw 2.371 2.440 ... (remaining 118500 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 391 or resid 393 through 610 or resid 801 thro \ ugh 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 610 or resid 801 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 391 or resid 393 through 610 or resid 801 thro \ ugh 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=0.50 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: 0.970 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: 5.950 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 42.780 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 0.369 15166 Z= 0.846 Angle : 1.036 15.992 20594 Z= 0.514 Chirality : 0.095 1.664 2343 Planarity : 0.007 0.074 2533 Dihedral : 15.040 91.607 5587 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.18 % Cbeta Deviations : 0.12 % 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: -3.88 (0.14), residues: 1792 helix: -2.65 (0.09), residues: 1166 sheet: -2.64 (0.57), residues: 63 loop : -1.87 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 203 HIS 0.005 0.001 HIS A 315 PHE 0.024 0.002 PHE C 180 TYR 0.026 0.002 TYR C 184 ARG 0.013 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7377 (pt0) REVERT: A 228 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7999 (tm-30) REVERT: A 241 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7443 (mm-40) REVERT: A 271 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8349 (Cg_exo) REVERT: A 581 LYS cc_start: 0.8792 (tttm) cc_final: 0.8502 (tptt) REVERT: B 263 TYR cc_start: 0.7835 (m-10) cc_final: 0.7578 (m-80) REVERT: B 271 PRO cc_start: 0.7872 (Cg_endo) cc_final: 0.7617 (Cg_exo) REVERT: B 305 ASN cc_start: 0.8387 (t0) cc_final: 0.8184 (t0) REVERT: B 422 GLN cc_start: 0.8427 (tt0) cc_final: 0.8002 (tt0) REVERT: B 524 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6687 (tm-30) REVERT: B 551 SER cc_start: 0.7782 (p) cc_final: 0.7479 (t) REVERT: C 240 TRP cc_start: 0.8072 (t-100) cc_final: 0.7556 (t60) REVERT: C 311 LEU cc_start: 0.8326 (mt) cc_final: 0.7733 (tt) REVERT: C 439 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7505 (ttt90) REVERT: C 497 LYS cc_start: 0.9232 (mmtp) cc_final: 0.8684 (mmmm) REVERT: C 607 MET cc_start: 0.6645 (mtp) cc_final: 0.6284 (mtm) REVERT: D 267 ASP cc_start: 0.8362 (t70) cc_final: 0.7492 (t0) REVERT: D 441 MET cc_start: 0.8447 (mmt) cc_final: 0.8065 (mmt) REVERT: D 466 MET cc_start: 0.8371 (mtm) cc_final: 0.8155 (mtp) REVERT: D 500 LYS cc_start: 0.8513 (pttp) cc_final: 0.8311 (pttm) REVERT: D 534 TYR cc_start: 0.8043 (m-10) cc_final: 0.7790 (m-10) REVERT: D 641 LYS cc_start: 0.7271 (mttt) cc_final: 0.6894 (tppt) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.2858 time to fit residues: 130.2810 Evaluate side-chains 215 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 562 ASN A 567 ASN B 196 GLN B 276 ASN B 317 ASN B 471 ASN C 237 ASN C 407 ASN C 425 GLN D 365 HIS D 423 GLN D 440 GLN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15166 Z= 0.160 Angle : 0.503 8.113 20594 Z= 0.261 Chirality : 0.039 0.147 2343 Planarity : 0.004 0.047 2533 Dihedral : 5.335 59.150 2092 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.61 % Allowed : 12.70 % Favored : 85.69 % 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: -0.88 (0.18), residues: 1792 helix: -0.12 (0.14), residues: 1157 sheet: -1.09 (0.65), residues: 51 loop : -1.27 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 231 HIS 0.006 0.001 HIS A 242 PHE 0.015 0.001 PHE D 516 TYR 0.013 0.001 TYR C 357 ARG 0.008 0.000 ARG B 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 1.847 Fit side-chains REVERT: A 228 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 240 TRP cc_start: 0.8436 (t-100) cc_final: 0.7677 (t60) REVERT: A 241 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7637 (mm110) REVERT: A 395 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7071 (mt) REVERT: A 422 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 581 LYS cc_start: 0.8710 (tttm) cc_final: 0.8326 (tptt) REVERT: A 607 MET cc_start: 0.7893 (mmt) cc_final: 0.7407 (mmm) REVERT: B 219 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7316 (mt) REVERT: B 418 ASP cc_start: 0.7556 (m-30) cc_final: 0.7316 (m-30) REVERT: B 422 GLN cc_start: 0.8366 (tt0) cc_final: 0.7936 (mt0) REVERT: B 524 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6782 (tm-30) REVERT: B 551 SER cc_start: 0.8202 (p) cc_final: 0.7834 (t) REVERT: B 575 ASP cc_start: 0.7521 (t0) cc_final: 0.7108 (t0) REVERT: C 241 GLN cc_start: 0.7945 (mp10) cc_final: 0.7287 (mp10) REVERT: C 311 LEU cc_start: 0.8268 (mt) cc_final: 0.7853 (tt) REVERT: C 422 GLN cc_start: 0.8616 (tp40) cc_final: 0.8352 (tp-100) REVERT: C 439 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7547 (ttt90) REVERT: C 481 ARG cc_start: 0.7874 (ptp-110) cc_final: 0.7326 (ptm160) REVERT: C 604 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8182 (mm-40) REVERT: D 267 ASP cc_start: 0.8433 (t70) cc_final: 0.7402 (t0) REVERT: D 268 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7949 (mtm) REVERT: D 641 LYS cc_start: 0.7264 (mttt) cc_final: 0.6897 (tppt) outliers start: 26 outliers final: 12 residues processed: 256 average time/residue: 0.2346 time to fit residues: 92.0670 Evaluate side-chains 223 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 0.0010 chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 161 optimal weight: 0.0670 chunk 55 optimal weight: 4.9990 chunk 130 optimal weight: 0.0570 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 305 ASN C 425 GLN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15166 Z= 0.124 Angle : 0.464 7.923 20594 Z= 0.240 Chirality : 0.039 0.147 2343 Planarity : 0.004 0.053 2533 Dihedral : 4.652 57.868 2092 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.67 % Allowed : 15.43 % Favored : 82.90 % 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: 0.36 (0.20), residues: 1792 helix: 0.90 (0.15), residues: 1154 sheet: -0.77 (0.69), residues: 46 loop : -0.89 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 316 HIS 0.005 0.001 HIS A 242 PHE 0.012 0.001 PHE C 180 TYR 0.014 0.001 TYR C 184 ARG 0.004 0.000 ARG B 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 224 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 240 TRP cc_start: 0.8431 (t-100) cc_final: 0.7700 (t60) REVERT: A 241 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7619 (mm110) REVERT: A 275 PHE cc_start: 0.8947 (m-10) cc_final: 0.8691 (m-80) REVERT: A 395 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.6895 (mt) REVERT: A 422 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 583 ASP cc_start: 0.6427 (m-30) cc_final: 0.6091 (m-30) REVERT: B 422 GLN cc_start: 0.8341 (tt0) cc_final: 0.7900 (mt0) REVERT: B 524 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6838 (tm-30) REVERT: B 551 SER cc_start: 0.8084 (p) cc_final: 0.7634 (t) REVERT: B 575 ASP cc_start: 0.7630 (t0) cc_final: 0.7135 (t0) REVERT: C 241 GLN cc_start: 0.8115 (mp10) cc_final: 0.7330 (mp10) REVERT: C 311 LEU cc_start: 0.8247 (mt) cc_final: 0.7886 (tt) REVERT: C 422 GLN cc_start: 0.8647 (tp40) cc_final: 0.8431 (tp-100) REVERT: C 439 ARG cc_start: 0.7938 (ttt90) cc_final: 0.7597 (ttt90) REVERT: C 481 ARG cc_start: 0.8091 (ptp-110) cc_final: 0.7433 (ptm160) REVERT: C 484 GLN cc_start: 0.8031 (mt0) cc_final: 0.7782 (mp10) REVERT: C 604 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8332 (mm-40) REVERT: D 267 ASP cc_start: 0.8366 (t70) cc_final: 0.7195 (t0) REVERT: D 268 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7886 (mtm) REVERT: D 641 LYS cc_start: 0.7262 (mttt) cc_final: 0.6865 (tppt) outliers start: 27 outliers final: 12 residues processed: 238 average time/residue: 0.2501 time to fit residues: 91.7656 Evaluate side-chains 224 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 458 CYS Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 84 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN C 299 ASN C 425 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: 0.7891 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15166 Z= 0.162 Angle : 0.466 7.776 20594 Z= 0.242 Chirality : 0.039 0.160 2343 Planarity : 0.004 0.057 2533 Dihedral : 4.353 58.108 2092 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.11 % Allowed : 16.79 % Favored : 81.10 % 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: 1.00 (0.20), residues: 1792 helix: 1.38 (0.15), residues: 1150 sheet: -0.63 (0.70), residues: 48 loop : -0.57 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 316 HIS 0.005 0.001 HIS A 242 PHE 0.013 0.001 PHE C 180 TYR 0.013 0.001 TYR C 357 ARG 0.002 0.000 ARG B 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 241 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7559 (mm110) REVERT: A 395 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7010 (mt) REVERT: A 405 ASN cc_start: 0.8190 (t0) cc_final: 0.7801 (t0) REVERT: A 422 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 493 GLU cc_start: 0.7527 (tp30) cc_final: 0.6860 (tp30) REVERT: A 581 LYS cc_start: 0.8700 (tttm) cc_final: 0.8494 (ttmt) REVERT: B 201 MET cc_start: 0.6880 (mmm) cc_final: 0.6652 (tpp) REVERT: B 219 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7358 (mt) REVERT: B 316 TRP cc_start: 0.8695 (m100) cc_final: 0.8431 (m100) REVERT: B 418 ASP cc_start: 0.7545 (t70) cc_final: 0.7296 (t0) REVERT: B 422 GLN cc_start: 0.8294 (tt0) cc_final: 0.7939 (mt0) REVERT: B 425 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: B 524 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6744 (tm-30) REVERT: B 551 SER cc_start: 0.7982 (p) cc_final: 0.7427 (t) REVERT: B 575 ASP cc_start: 0.7643 (t0) cc_final: 0.7236 (t0) REVERT: C 235 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7128 (p0) REVERT: C 241 GLN cc_start: 0.8190 (mp10) cc_final: 0.7679 (mp10) REVERT: C 311 LEU cc_start: 0.8246 (mt) cc_final: 0.7868 (tp) REVERT: C 439 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7571 (ttt90) REVERT: C 481 ARG cc_start: 0.8045 (ptp-110) cc_final: 0.7435 (ptm160) REVERT: C 484 GLN cc_start: 0.7996 (mt0) cc_final: 0.7780 (mt0) REVERT: D 267 ASP cc_start: 0.8344 (t70) cc_final: 0.7196 (t0) REVERT: D 268 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7891 (mtm) REVERT: D 641 LYS cc_start: 0.7267 (mttt) cc_final: 0.6879 (tppt) outliers start: 34 outliers final: 18 residues processed: 235 average time/residue: 0.2375 time to fit residues: 85.6585 Evaluate side-chains 225 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 458 CYS Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** B 317 ASN C 422 GLN C 425 GLN C 604 GLN D 440 GLN ** D 453 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: 0.7981 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15166 Z= 0.296 Angle : 0.550 8.715 20594 Z= 0.287 Chirality : 0.042 0.180 2343 Planarity : 0.004 0.048 2533 Dihedral : 4.483 59.690 2092 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.85 % Allowed : 17.22 % Favored : 79.93 % 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: 1.03 (0.20), residues: 1792 helix: 1.38 (0.15), residues: 1148 sheet: -0.68 (0.71), residues: 48 loop : -0.49 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 316 HIS 0.004 0.001 HIS A 242 PHE 0.017 0.001 PHE C 301 TYR 0.022 0.001 TYR D 351 ARG 0.003 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 241 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7675 (mm110) REVERT: A 395 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7460 (mt) REVERT: A 422 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 581 LYS cc_start: 0.8779 (tttm) cc_final: 0.8563 (tptt) REVERT: B 300 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6724 (tmm) REVERT: B 305 ASN cc_start: 0.8615 (t0) cc_final: 0.8397 (t0) REVERT: B 316 TRP cc_start: 0.9005 (m100) cc_final: 0.8748 (m100) REVERT: B 418 ASP cc_start: 0.7586 (t70) cc_final: 0.7283 (t0) REVERT: B 422 GLN cc_start: 0.8341 (tt0) cc_final: 0.7989 (mt0) REVERT: B 425 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: B 575 ASP cc_start: 0.7691 (t0) cc_final: 0.7239 (t0) REVERT: C 184 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: C 235 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7285 (p0) REVERT: C 241 GLN cc_start: 0.8222 (mp10) cc_final: 0.7691 (mp10) REVERT: C 311 LEU cc_start: 0.8303 (mt) cc_final: 0.7900 (tt) REVERT: C 439 ARG cc_start: 0.8180 (ttt90) cc_final: 0.7629 (ttt90) REVERT: C 481 ARG cc_start: 0.8074 (ptp-110) cc_final: 0.7588 (ptm160) REVERT: C 484 GLN cc_start: 0.8063 (mt0) cc_final: 0.7849 (mt0) REVERT: D 267 ASP cc_start: 0.8391 (t70) cc_final: 0.7223 (t0) REVERT: D 641 LYS cc_start: 0.7298 (mttt) cc_final: 0.7040 (tppt) outliers start: 46 outliers final: 30 residues processed: 234 average time/residue: 0.2444 time to fit residues: 87.3065 Evaluate side-chains 232 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 458 CYS Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 0.0980 chunk 34 optimal weight: 0.0870 chunk 101 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.0980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN B 422 GLN C 422 GLN C 425 GLN D 276 GLN D 453 ASN ** 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: 0.7897 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15166 Z= 0.129 Angle : 0.466 8.061 20594 Z= 0.241 Chirality : 0.039 0.156 2343 Planarity : 0.003 0.052 2533 Dihedral : 4.183 56.151 2092 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.80 % Allowed : 18.71 % Favored : 79.49 % 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: 1.46 (0.21), residues: 1792 helix: 1.75 (0.16), residues: 1148 sheet: -0.46 (0.72), residues: 48 loop : -0.40 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 316 HIS 0.005 0.001 HIS A 242 PHE 0.009 0.001 PHE C 180 TYR 0.024 0.001 TYR D 229 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 241 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7548 (mm110) REVERT: A 395 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7039 (mt) REVERT: A 422 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 493 GLU cc_start: 0.7576 (tp30) cc_final: 0.6669 (tp30) REVERT: A 581 LYS cc_start: 0.8733 (tttm) cc_final: 0.8500 (ttmt) REVERT: A 583 ASP cc_start: 0.6329 (m-30) cc_final: 0.6031 (m-30) REVERT: B 305 ASN cc_start: 0.8441 (t0) cc_final: 0.8178 (t0) REVERT: B 418 ASP cc_start: 0.7554 (t70) cc_final: 0.7262 (t0) REVERT: B 422 GLN cc_start: 0.8206 (tt0) cc_final: 0.7959 (mt0) REVERT: B 425 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: B 519 MET cc_start: 0.7468 (tpp) cc_final: 0.6907 (tpp) REVERT: B 575 ASP cc_start: 0.7747 (t0) cc_final: 0.7313 (t0) REVERT: C 193 ASP cc_start: 0.8092 (t0) cc_final: 0.7869 (t0) REVERT: C 241 GLN cc_start: 0.8216 (mp10) cc_final: 0.7664 (mp10) REVERT: C 246 THR cc_start: 0.8469 (m) cc_final: 0.8167 (p) REVERT: C 311 LEU cc_start: 0.8257 (mt) cc_final: 0.8034 (tp) REVERT: C 439 ARG cc_start: 0.8129 (ttt90) cc_final: 0.7627 (ttt90) REVERT: C 481 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7542 (ptm160) REVERT: C 604 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7728 (mm-40) REVERT: D 267 ASP cc_start: 0.8294 (t70) cc_final: 0.7145 (t0) REVERT: D 641 LYS cc_start: 0.7240 (mttt) cc_final: 0.6854 (tppt) outliers start: 29 outliers final: 19 residues processed: 242 average time/residue: 0.2390 time to fit residues: 88.2442 Evaluate side-chains 234 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 213 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 458 CYS Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 126 optimal weight: 0.0030 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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** C 422 GLN C 425 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 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: 0.7973 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15166 Z= 0.279 Angle : 0.542 8.271 20594 Z= 0.283 Chirality : 0.042 0.182 2343 Planarity : 0.004 0.054 2533 Dihedral : 4.256 49.374 2092 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.42 % Allowed : 19.02 % Favored : 78.56 % 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: 1.31 (0.21), residues: 1792 helix: 1.60 (0.16), residues: 1150 sheet: -0.54 (0.72), residues: 48 loop : -0.38 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 316 HIS 0.003 0.001 HIS A 242 PHE 0.016 0.001 PHE C 301 TYR 0.030 0.001 TYR D 229 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 241 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7644 (mm110) REVERT: A 395 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7339 (mt) REVERT: A 422 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 581 LYS cc_start: 0.8770 (tttm) cc_final: 0.8444 (tptt) REVERT: A 583 ASP cc_start: 0.6357 (m-30) cc_final: 0.6050 (m-30) REVERT: B 268 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8110 (t) REVERT: B 305 ASN cc_start: 0.8590 (t0) cc_final: 0.8269 (t0) REVERT: B 418 ASP cc_start: 0.7637 (t70) cc_final: 0.7345 (t0) REVERT: B 422 GLN cc_start: 0.8255 (tt0) cc_final: 0.7985 (mt0) REVERT: B 425 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: B 519 MET cc_start: 0.7500 (tpp) cc_final: 0.7013 (tpp) REVERT: B 575 ASP cc_start: 0.7808 (t0) cc_final: 0.7384 (t0) REVERT: C 184 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: C 235 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.6809 (t70) REVERT: C 311 LEU cc_start: 0.8310 (mt) cc_final: 0.7917 (tt) REVERT: C 439 ARG cc_start: 0.8244 (ttt90) cc_final: 0.7607 (ttt90) REVERT: C 481 ARG cc_start: 0.7966 (ptp-110) cc_final: 0.7567 (ptm160) REVERT: C 484 GLN cc_start: 0.8227 (mt0) cc_final: 0.7682 (mp10) REVERT: C 604 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8328 (mm-40) REVERT: D 267 ASP cc_start: 0.8358 (t70) cc_final: 0.7201 (t0) REVERT: D 641 LYS cc_start: 0.7350 (mttt) cc_final: 0.7042 (tppt) outliers start: 39 outliers final: 26 residues processed: 231 average time/residue: 0.2375 time to fit residues: 84.5316 Evaluate side-chains 235 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 523 ASN A 554 ASN C 425 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 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: 0.7931 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15166 Z= 0.177 Angle : 0.493 7.792 20594 Z= 0.257 Chirality : 0.040 0.185 2343 Planarity : 0.003 0.045 2533 Dihedral : 4.008 35.840 2092 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.11 % Allowed : 19.21 % Favored : 78.69 % 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: 1.47 (0.21), residues: 1792 helix: 1.73 (0.16), residues: 1150 sheet: -0.50 (0.72), residues: 48 loop : -0.33 (0.28), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 316 HIS 0.004 0.001 HIS A 242 PHE 0.011 0.001 PHE C 483 TYR 0.031 0.001 TYR D 229 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 1.726 Fit side-chains REVERT: A 228 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 395 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7175 (mt) REVERT: A 422 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 508 TYR cc_start: 0.8642 (m-80) cc_final: 0.8418 (m-80) REVERT: A 581 LYS cc_start: 0.8747 (tttm) cc_final: 0.8432 (tptt) REVERT: A 583 ASP cc_start: 0.6281 (m-30) cc_final: 0.5967 (m-30) REVERT: B 300 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6711 (tmm) REVERT: B 305 ASN cc_start: 0.8487 (t0) cc_final: 0.8223 (t0) REVERT: B 418 ASP cc_start: 0.7597 (t70) cc_final: 0.7325 (t0) REVERT: B 519 MET cc_start: 0.7501 (tpp) cc_final: 0.7040 (tpp) REVERT: C 184 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6555 (m-80) REVERT: C 235 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.6758 (t70) REVERT: C 241 GLN cc_start: 0.8222 (mp10) cc_final: 0.7650 (mp10) REVERT: C 246 THR cc_start: 0.8370 (m) cc_final: 0.8082 (p) REVERT: C 311 LEU cc_start: 0.8288 (mt) cc_final: 0.7942 (tt) REVERT: C 439 ARG cc_start: 0.8227 (ttt90) cc_final: 0.7592 (ttt90) REVERT: C 481 ARG cc_start: 0.7934 (ptp-110) cc_final: 0.7518 (ptm160) REVERT: C 484 GLN cc_start: 0.8177 (mt0) cc_final: 0.7670 (mp10) REVERT: C 604 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8298 (mm-40) REVERT: D 267 ASP cc_start: 0.8340 (t70) cc_final: 0.7117 (t0) REVERT: D 474 LEU cc_start: 0.8104 (tp) cc_final: 0.7843 (mt) REVERT: D 641 LYS cc_start: 0.7314 (mttt) cc_final: 0.7004 (tppt) outliers start: 34 outliers final: 23 residues processed: 232 average time/residue: 0.2324 time to fit residues: 82.9576 Evaluate side-chains 225 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 145 optimal weight: 0.0870 chunk 152 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 422 GLN C 425 GLN ** C 484 GLN ** 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: 0.7899 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15166 Z= 0.145 Angle : 0.484 9.456 20594 Z= 0.253 Chirality : 0.039 0.173 2343 Planarity : 0.003 0.049 2533 Dihedral : 3.768 17.965 2092 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.67 % Allowed : 19.83 % Favored : 78.50 % 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: 1.64 (0.21), residues: 1792 helix: 1.86 (0.16), residues: 1150 sheet: -0.25 (0.72), residues: 48 loop : -0.28 (0.28), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 316 HIS 0.004 0.001 HIS A 242 PHE 0.019 0.001 PHE C 483 TYR 0.030 0.001 TYR D 229 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: A 395 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.6976 (mt) REVERT: A 422 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 425 GLN cc_start: 0.8335 (tp40) cc_final: 0.8132 (mm-40) REVERT: A 581 LYS cc_start: 0.8736 (tttm) cc_final: 0.8380 (tptt) REVERT: A 583 ASP cc_start: 0.6360 (m-30) cc_final: 0.5962 (m-30) REVERT: B 305 ASN cc_start: 0.8459 (t0) cc_final: 0.8219 (t0) REVERT: B 418 ASP cc_start: 0.7596 (t70) cc_final: 0.7318 (t0) REVERT: B 519 MET cc_start: 0.7488 (tpp) cc_final: 0.7032 (tpp) REVERT: B 575 ASP cc_start: 0.7771 (t0) cc_final: 0.7400 (t0) REVERT: C 184 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: C 246 THR cc_start: 0.8380 (m) cc_final: 0.8104 (p) REVERT: C 311 LEU cc_start: 0.8276 (mt) cc_final: 0.7960 (tt) REVERT: C 439 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7617 (ttt90) REVERT: C 481 ARG cc_start: 0.7829 (ptp-110) cc_final: 0.7390 (ptm160) REVERT: C 484 GLN cc_start: 0.8078 (mt0) cc_final: 0.7793 (mp10) REVERT: C 595 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8793 (mmmt) REVERT: C 604 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8265 (mm-40) REVERT: D 267 ASP cc_start: 0.8288 (t70) cc_final: 0.7043 (t0) REVERT: D 474 LEU cc_start: 0.7997 (tp) cc_final: 0.7754 (mt) REVERT: D 641 LYS cc_start: 0.7232 (mttt) cc_final: 0.6839 (tppt) outliers start: 27 outliers final: 17 residues processed: 229 average time/residue: 0.2427 time to fit residues: 85.1448 Evaluate side-chains 217 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.0020 chunk 80 optimal weight: 0.3980 chunk 118 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 473 HIS C 425 GLN ** C 484 GLN ** 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: 0.7897 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15166 Z= 0.152 Angle : 0.494 7.563 20594 Z= 0.258 Chirality : 0.040 0.190 2343 Planarity : 0.003 0.048 2533 Dihedral : 3.735 17.303 2092 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.36 % Allowed : 20.38 % Favored : 78.25 % 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: 1.70 (0.21), residues: 1792 helix: 1.93 (0.16), residues: 1147 sheet: -0.03 (0.73), residues: 48 loop : -0.31 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 316 HIS 0.004 0.001 HIS A 242 PHE 0.026 0.001 PHE C 483 TYR 0.029 0.001 TYR D 229 ARG 0.003 0.000 ARG C 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 395 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.6974 (mt) REVERT: A 422 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 455 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7961 (mt-10) REVERT: A 581 LYS cc_start: 0.8741 (tttm) cc_final: 0.8395 (tptt) REVERT: A 586 GLU cc_start: 0.8201 (tp30) cc_final: 0.7890 (tt0) REVERT: B 305 ASN cc_start: 0.8436 (t0) cc_final: 0.8183 (t0) REVERT: B 418 ASP cc_start: 0.7603 (t70) cc_final: 0.7317 (t0) REVERT: B 519 MET cc_start: 0.7504 (tpp) cc_final: 0.7109 (tpt) REVERT: C 184 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: C 246 THR cc_start: 0.8380 (m) cc_final: 0.8107 (p) REVERT: C 311 LEU cc_start: 0.8283 (mt) cc_final: 0.7963 (tt) REVERT: C 434 GLU cc_start: 0.7587 (tt0) cc_final: 0.7285 (mt-10) REVERT: C 439 ARG cc_start: 0.8181 (ttt90) cc_final: 0.7615 (ttt90) REVERT: C 481 ARG cc_start: 0.7717 (ptp-110) cc_final: 0.7350 (ptm160) REVERT: C 484 GLN cc_start: 0.7968 (mt0) cc_final: 0.7744 (mp10) REVERT: C 604 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8277 (mm-40) REVERT: D 474 LEU cc_start: 0.7993 (tp) cc_final: 0.7746 (mt) REVERT: D 641 LYS cc_start: 0.7210 (mttt) cc_final: 0.6966 (tppt) outliers start: 22 outliers final: 18 residues processed: 220 average time/residue: 0.2326 time to fit residues: 78.6182 Evaluate side-chains 220 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 146 optimal weight: 0.0770 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN C 425 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121558 restraints weight = 23795.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123032 restraints weight = 20158.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124062 restraints weight = 15917.355| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15166 Z= 0.161 Angle : 0.503 10.768 20594 Z= 0.260 Chirality : 0.040 0.204 2343 Planarity : 0.003 0.044 2533 Dihedral : 3.714 17.289 2092 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.67 % Allowed : 19.95 % Favored : 78.38 % 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: 1.76 (0.21), residues: 1792 helix: 1.96 (0.16), residues: 1143 sheet: 0.15 (0.76), residues: 48 loop : -0.25 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 316 HIS 0.004 0.001 HIS A 242 PHE 0.025 0.001 PHE C 483 TYR 0.028 0.001 TYR D 229 ARG 0.003 0.000 ARG C 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.32 seconds wall clock time: 54 minutes 25.80 seconds (3265.80 seconds total)