Starting phenix.real_space_refine on Fri Feb 16 07:30:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev8_28622/02_2024/8ev8_28622_neut_updated.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 9609 2.51 5 N 2401 2.21 5 O 2668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 162": "OD1" <-> "OD2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" 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 TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B 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 ASP 235": "OD1" <-> "OD2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B ASP 462": "OD1" <-> "OD2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 507": "OD1" <-> "OD2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B ASP 532": "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 TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 260": "OD1" <-> "OD2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C ASP 475": "OD1" <-> "OD2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 583": "OD1" <-> "OD2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C ASP 609": "OD1" <-> "OD2" 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 TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 346": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 494": "OD1" <-> "OD2" Residue "D ASP 513": "OD1" <-> "OD2" Residue "D ASP 523": "OD1" <-> "OD2" Residue "D ASP 529": "OD1" <-> "OD2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 576": "OD1" <-> "OD2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 620": "OD1" <-> "OD2" Residue "D GLU 626": "OE1" <-> "OE2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3675 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 449, 3664 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 449, 3664 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain breaks: 1 bond proxies already assigned to first conformer: 3733 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3632 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 14, 'TRANS': 430} Chain breaks: 1 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: 3610 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Conformer: "B" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} bond proxies already assigned to first conformer: 3684 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.70 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.30 Time building chain proxies: 11.24, per 1000 atoms: 0.76 Number of scatterers: 14748 At special positions: 0 Unit cell: (107.9, 112.88, 131.97, 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 2668 8.00 N 2401 7.00 C 9609 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: 5.32 Conformation dependent library (CDL) restraints added in 4.0 seconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 9 sheets defined 59.8% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 167 through 192 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 195 through 198 No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 200 through 223 removed outlier: 3.690A pdb=" N ARG A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.597A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.629A 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 549 through 553 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 592 through 609 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 256 Processing helix chain 'B' and resid 271 through 279 removed outlier: 4.197A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 298 through 328 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 375 through 406 Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 431 through 446 Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.469A pdb=" N LYS B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 477 removed outlier: 6.164A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) 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 223 removed outlier: 3.787A pdb=" N ARG C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) 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 271 through 279 removed outlier: 4.490A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 298 through 328 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 375 through 406 Processing helix chain 'C' and resid 408 through 426 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 453 through 459 removed outlier: 4.953A pdb=" N SER C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 479 removed outlier: 6.088A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS C 479 " --> pdb=" O ASP C 475 " (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 298 through 306 removed outlier: 3.697A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.704A pdb=" N LEU D 315 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE D 317 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.719A 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 378 Processing helix chain 'D' and resid 393 through 405 Processing helix chain 'D' and resid 417 through 448 Processing helix chain 'D' and resid 450 through 468 Processing helix chain 'D' and resid 473 through 489 Processing helix chain 'D' and resid 496 through 501 removed outlier: 4.435A pdb=" N THR D 501 " --> pdb=" O ASP D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 520 removed outlier: 3.618A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.400A 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 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 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 Processing sheet with id= B, first strand: chain 'A' and resid 567 through 570 removed outlier: 3.612A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 539 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 499 through 503 Processing sheet with id= D, first strand: chain 'B' and resid 527 through 530 removed outlier: 3.969A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (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 527 through 530 removed outlier: 3.892A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.034A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.737A pdb=" N SER D 588 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 607 through 610 removed outlier: 3.995A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2373 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: 4.60 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4546 1.34 - 1.46: 3082 1.46 - 1.58: 7369 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 15102 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 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 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 3.40e+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 3.38e+02 bond pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " ideal model delta sigma weight residual 1.808 1.532 0.276 2.00e-02 2.50e+03 1.90e+02 ... (remaining 15097 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.95: 275 105.95 - 113.94: 8631 113.94 - 121.93: 8941 121.93 - 129.93: 2556 129.93 - 137.92: 102 Bond angle restraints: 20505 Sorted by residual: angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 128.15 -15.92 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 112.23 128.11 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 112.23 128.10 -15.87 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 112.23 128.06 -15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C2 PCG B 802 " pdb=" N3 PCG B 802 " pdb=" C4 PCG B 802 " ideal model delta sigma weight residual 120.18 106.88 13.30 3.00e+00 1.11e-01 1.97e+01 ... (remaining 20500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7881 17.61 - 35.21: 854 35.21 - 52.82: 184 52.82 - 70.42: 31 70.42 - 88.03: 12 Dihedral angle restraints: 8962 sinusoidal: 3679 harmonic: 5283 Sorted by residual: dihedral pdb=" CA PHE C 192 " pdb=" C PHE C 192 " pdb=" N ASP C 193 " pdb=" CA ASP C 193 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU C 227 " pdb=" C LEU C 227 " pdb=" N GLU C 228 " pdb=" CA GLU C 228 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LEU B 227 " pdb=" C LEU B 227 " pdb=" N GLU B 228 " pdb=" CA GLU B 228 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 8959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2321 0.336 - 0.672: 8 0.672 - 1.008: 0 1.008 - 1.344: 0 1.344 - 1.681: 4 Chirality restraints: 2333 Sorted by residual: chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.06e+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 -0.72 -1.68 2.00e-01 2.50e+01 7.04e+01 ... (remaining 2330 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO D 273 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 502 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO D 503 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 503 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 503 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 411 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO D 412 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 412 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 412 " -0.033 5.00e-02 4.00e+02 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3556 2.79 - 3.31: 13398 3.31 - 3.84: 25681 3.84 - 4.37: 29455 4.37 - 4.90: 50810 Nonbonded interactions: 122900 Sorted by model distance: nonbonded pdb=" O THR C 360 " pdb=" OG1 THR C 364 " model vdw 2.257 2.440 nonbonded pdb=" O SER B 551 " pdb=" OD1 ASN B 562 " model vdw 2.308 3.040 nonbonded pdb=" O THR B 360 " pdb=" OG1 THR B 364 " model vdw 2.313 2.440 nonbonded pdb=" O LEU C 195 " pdb=" NE1 TRP C 203 " model vdw 2.331 2.520 nonbonded pdb=" ND2 ASN B 317 " pdb=" OD1 ASP B 384 " model vdw 2.333 2.520 ... (remaining 122895 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 260 or resid 270 through 391 or resid 393 thro \ ugh 611 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 611 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 611 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.120 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 44.860 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 15102 Z= 0.790 Angle : 0.893 15.922 20505 Z= 0.425 Chirality : 0.092 1.681 2333 Planarity : 0.006 0.066 2523 Dihedral : 15.191 88.028 5568 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.93 % Allowed : 12.00 % Favored : 87.07 % 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: -2.52 (0.16), residues: 1781 helix: -1.60 (0.11), residues: 1152 sheet: -2.06 (0.59), residues: 55 loop : -1.36 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 171 HIS 0.004 0.001 HIS A 473 PHE 0.016 0.002 PHE B 426 TYR 0.016 0.002 TYR C 263 ARG 0.005 0.000 ARG C 603 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 1.620 Fit side-chains REVERT: C 418 ASP cc_start: 0.8157 (m-30) cc_final: 0.7942 (m-30) REVERT: C 515 ILE cc_start: 0.8906 (mm) cc_final: 0.8671 (mm) REVERT: D 249 ASN cc_start: 0.7504 (t0) cc_final: 0.7070 (t0) outliers start: 15 outliers final: 5 residues processed: 223 average time/residue: 0.3201 time to fit residues: 100.0823 Evaluate side-chains 151 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain C residue 563 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 296 ASN A 562 ASN A 610 ASN B 196 GLN B 229 GLN B 242 HIS B 276 ASN B 407 ASN C 241 GLN C 248 GLN C 317 ASN C 398 ASN C 471 ASN C 473 HIS C 554 ASN D 230 ASN D 232 ASN D 340 HIS D 365 HIS D 367 ASN D 423 GLN D 426 ASN D 440 GLN D 531 GLN D 602 ASN D 630 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15102 Z= 0.162 Angle : 0.461 7.395 20505 Z= 0.245 Chirality : 0.039 0.197 2333 Planarity : 0.004 0.047 2523 Dihedral : 5.139 57.357 2095 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.37 % Allowed : 14.73 % Favored : 83.90 % 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: -0.19 (0.19), residues: 1781 helix: 0.42 (0.14), residues: 1126 sheet: -1.58 (0.61), residues: 55 loop : -0.85 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 171 HIS 0.003 0.001 HIS B 315 PHE 0.019 0.001 PHE D 310 TYR 0.011 0.001 TYR B 354 ARG 0.007 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 169 time to evaluate : 1.611 Fit side-chains REVERT: B 232 MET cc_start: 0.7788 (tpp) cc_final: 0.7168 (tpp) REVERT: D 249 ASN cc_start: 0.7321 (t0) cc_final: 0.6829 (t0) REVERT: D 393 GLU cc_start: 0.7917 (mp0) cc_final: 0.7712 (mp0) REVERT: D 536 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7127 (ptp) outliers start: 22 outliers final: 13 residues processed: 183 average time/residue: 0.2522 time to fit residues: 69.7533 Evaluate side-chains 161 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN B 248 GLN C 229 GLN C 241 GLN C 345 HIS C 554 ASN D 440 GLN D 630 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15102 Z= 0.174 Angle : 0.452 7.704 20505 Z= 0.240 Chirality : 0.039 0.214 2333 Planarity : 0.004 0.042 2523 Dihedral : 4.401 47.314 2087 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.86 % Allowed : 15.41 % Favored : 82.72 % 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: 0.73 (0.20), residues: 1781 helix: 1.15 (0.15), residues: 1134 sheet: -0.81 (0.59), residues: 59 loop : -0.57 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.005 0.001 HIS D 365 PHE 0.014 0.001 PHE C 192 TYR 0.011 0.001 TYR C 354 ARG 0.007 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.575 Fit side-chains REVERT: A 543 ASP cc_start: 0.7538 (t0) cc_final: 0.7165 (t0) REVERT: B 232 MET cc_start: 0.7743 (tpp) cc_final: 0.7174 (tpp) REVERT: D 249 ASN cc_start: 0.7307 (t0) cc_final: 0.6880 (t0) REVERT: D 424 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8346 (tp) outliers start: 30 outliers final: 20 residues processed: 188 average time/residue: 0.2533 time to fit residues: 72.3844 Evaluate side-chains 175 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 0.0570 chunk 76 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN B 473 HIS C 241 GLN D 630 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15102 Z= 0.121 Angle : 0.416 7.450 20505 Z= 0.221 Chirality : 0.038 0.197 2333 Planarity : 0.003 0.041 2523 Dihedral : 3.983 45.844 2083 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.93 % Allowed : 16.10 % Favored : 81.98 % 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: 1.50 (0.20), residues: 1781 helix: 1.77 (0.15), residues: 1125 sheet: -0.95 (0.61), residues: 55 loop : -0.22 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 PHE 0.011 0.001 PHE A 426 TYR 0.010 0.001 TYR C 357 ARG 0.006 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 1.654 Fit side-chains REVERT: A 467 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 501 THR cc_start: 0.8252 (p) cc_final: 0.7973 (t) REVERT: A 543 ASP cc_start: 0.7483 (t0) cc_final: 0.7144 (t0) REVERT: C 515 ILE cc_start: 0.8983 (mm) cc_final: 0.8708 (mm) REVERT: D 249 ASN cc_start: 0.7249 (t0) cc_final: 0.6869 (t0) REVERT: D 424 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8207 (tp) outliers start: 31 outliers final: 16 residues processed: 206 average time/residue: 0.2404 time to fit residues: 76.0261 Evaluate side-chains 179 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS A 610 ASN C 241 GLN D 301 GLN D 630 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15102 Z= 0.242 Angle : 0.490 9.071 20505 Z= 0.255 Chirality : 0.041 0.255 2333 Planarity : 0.004 0.040 2523 Dihedral : 4.137 49.779 2083 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.80 % Allowed : 16.59 % Favored : 81.60 % 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: 1.48 (0.20), residues: 1781 helix: 1.69 (0.15), residues: 1127 sheet: -0.58 (0.56), residues: 69 loop : -0.13 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 445 HIS 0.005 0.001 HIS D 365 PHE 0.018 0.001 PHE C 192 TYR 0.014 0.001 TYR C 354 ARG 0.005 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.773 Fit side-chains REVERT: A 184 TYR cc_start: 0.7374 (m-80) cc_final: 0.7087 (m-80) REVERT: A 543 ASP cc_start: 0.7490 (t0) cc_final: 0.7163 (t0) REVERT: C 515 ILE cc_start: 0.9016 (mm) cc_final: 0.8746 (mm) REVERT: D 249 ASN cc_start: 0.7462 (t0) cc_final: 0.7048 (t0) REVERT: D 424 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8419 (tp) outliers start: 29 outliers final: 23 residues processed: 185 average time/residue: 0.2448 time to fit residues: 69.3604 Evaluate side-chains 179 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN C 241 GLN D 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15102 Z= 0.164 Angle : 0.453 11.425 20505 Z= 0.236 Chirality : 0.039 0.223 2333 Planarity : 0.003 0.040 2523 Dihedral : 3.997 48.796 2083 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.80 % Allowed : 17.09 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1781 helix: 1.86 (0.15), residues: 1133 sheet: -0.05 (0.62), residues: 59 loop : -0.06 (0.28), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.005 0.001 HIS D 251 PHE 0.012 0.001 PHE A 192 TYR 0.012 0.001 TYR B 243 ARG 0.007 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.723 Fit side-chains REVERT: A 184 TYR cc_start: 0.7482 (m-80) cc_final: 0.7185 (m-80) REVERT: A 501 THR cc_start: 0.8269 (p) cc_final: 0.7871 (t) REVERT: A 543 ASP cc_start: 0.7495 (t0) cc_final: 0.7184 (t0) REVERT: C 515 ILE cc_start: 0.9020 (mm) cc_final: 0.8748 (mm) REVERT: D 249 ASN cc_start: 0.7414 (t0) cc_final: 0.7077 (t0) REVERT: D 424 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8322 (tp) outliers start: 29 outliers final: 26 residues processed: 178 average time/residue: 0.2441 time to fit residues: 66.5273 Evaluate side-chains 179 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 170 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN C 241 GLN D 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15102 Z= 0.258 Angle : 0.494 9.581 20505 Z= 0.257 Chirality : 0.041 0.249 2333 Planarity : 0.003 0.040 2523 Dihedral : 4.163 51.554 2083 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 16.66 % Favored : 81.17 % 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: 1.55 (0.20), residues: 1781 helix: 1.71 (0.15), residues: 1133 sheet: -0.28 (0.58), residues: 69 loop : -0.06 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.006 0.001 HIS D 365 PHE 0.017 0.001 PHE C 192 TYR 0.014 0.001 TYR C 354 ARG 0.005 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.658 Fit side-chains REVERT: A 543 ASP cc_start: 0.7535 (t0) cc_final: 0.7226 (t0) REVERT: B 471 ASN cc_start: 0.8313 (t0) cc_final: 0.8080 (t0) REVERT: C 162 ASP cc_start: 0.8120 (t0) cc_final: 0.7881 (t0) REVERT: C 515 ILE cc_start: 0.9036 (mm) cc_final: 0.8777 (mm) REVERT: D 249 ASN cc_start: 0.7462 (t0) cc_final: 0.7026 (t0) REVERT: D 424 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8410 (tp) outliers start: 35 outliers final: 31 residues processed: 185 average time/residue: 0.2495 time to fit residues: 71.7615 Evaluate side-chains 188 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 594 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN D 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15102 Z= 0.153 Angle : 0.442 8.691 20505 Z= 0.231 Chirality : 0.039 0.221 2333 Planarity : 0.003 0.040 2523 Dihedral : 3.981 49.253 2083 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.05 % Allowed : 16.97 % Favored : 80.98 % 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: 1.88 (0.20), residues: 1781 helix: 1.96 (0.15), residues: 1133 sheet: 0.15 (0.64), residues: 59 loop : 0.04 (0.28), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 171 HIS 0.005 0.001 HIS D 251 PHE 0.011 0.001 PHE A 192 TYR 0.010 0.001 TYR C 357 ARG 0.005 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 1.525 Fit side-chains REVERT: A 501 THR cc_start: 0.8205 (p) cc_final: 0.7789 (t) REVERT: A 543 ASP cc_start: 0.7486 (t0) cc_final: 0.7147 (t0) REVERT: B 471 ASN cc_start: 0.8318 (t0) cc_final: 0.8115 (t0) REVERT: C 515 ILE cc_start: 0.9059 (mm) cc_final: 0.8801 (mm) REVERT: D 214 THR cc_start: 0.8211 (p) cc_final: 0.8003 (t) REVERT: D 424 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 33 outliers final: 29 residues processed: 184 average time/residue: 0.2440 time to fit residues: 68.6162 Evaluate side-chains 185 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 594 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN D 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15102 Z= 0.139 Angle : 0.436 8.504 20505 Z= 0.228 Chirality : 0.039 0.191 2333 Planarity : 0.003 0.039 2523 Dihedral : 3.892 47.760 2083 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.99 % Allowed : 16.84 % Favored : 81.17 % 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: 2.05 (0.21), residues: 1781 helix: 2.10 (0.15), residues: 1132 sheet: 0.23 (0.64), residues: 59 loop : 0.09 (0.28), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.005 0.001 HIS D 251 PHE 0.012 0.001 PHE D 590 TYR 0.012 0.001 TYR D 252 ARG 0.005 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.632 Fit side-chains REVERT: A 501 THR cc_start: 0.8123 (p) cc_final: 0.7698 (t) REVERT: A 543 ASP cc_start: 0.7521 (t0) cc_final: 0.7280 (t70) REVERT: C 515 ILE cc_start: 0.9075 (mm) cc_final: 0.8837 (mm) REVERT: D 214 THR cc_start: 0.8178 (p) cc_final: 0.7966 (t) REVERT: D 249 ASN cc_start: 0.7563 (t0) cc_final: 0.7212 (t0) REVERT: D 424 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8290 (tp) REVERT: D 631 TYR cc_start: 0.8482 (m-80) cc_final: 0.8038 (m-80) outliers start: 32 outliers final: 29 residues processed: 183 average time/residue: 0.2366 time to fit residues: 67.3334 Evaluate side-chains 185 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 594 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 162 optimal weight: 0.0070 chunk 140 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 471 ASN D 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15102 Z= 0.133 Angle : 0.440 8.670 20505 Z= 0.230 Chirality : 0.039 0.179 2333 Planarity : 0.003 0.039 2523 Dihedral : 3.844 47.239 2083 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.68 % Allowed : 17.46 % Favored : 80.86 % 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: 2.16 (0.21), residues: 1781 helix: 2.19 (0.15), residues: 1127 sheet: 0.50 (0.66), residues: 54 loop : 0.12 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.006 0.001 HIS D 251 PHE 0.010 0.001 PHE D 590 TYR 0.010 0.001 TYR A 546 ARG 0.005 0.000 ARG D 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.698 Fit side-chains REVERT: A 501 THR cc_start: 0.8134 (p) cc_final: 0.7687 (t) REVERT: A 543 ASP cc_start: 0.7498 (t0) cc_final: 0.7270 (t70) REVERT: B 232 MET cc_start: 0.7279 (ttp) cc_final: 0.7043 (ttm) REVERT: C 193 ASP cc_start: 0.7470 (t70) cc_final: 0.6949 (t0) REVERT: C 515 ILE cc_start: 0.9071 (mm) cc_final: 0.8832 (mm) REVERT: D 214 THR cc_start: 0.8156 (p) cc_final: 0.7945 (t) REVERT: D 249 ASN cc_start: 0.7557 (t0) cc_final: 0.7234 (t0) REVERT: D 424 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8227 (tp) REVERT: D 631 TYR cc_start: 0.8442 (m-80) cc_final: 0.8062 (m-80) outliers start: 27 outliers final: 24 residues processed: 179 average time/residue: 0.2334 time to fit residues: 64.7859 Evaluate side-chains 180 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 594 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 25 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.156842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121942 restraints weight = 25036.345| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.89 r_work: 0.2858 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15102 Z= 0.115 Angle : 0.426 8.863 20505 Z= 0.222 Chirality : 0.038 0.158 2333 Planarity : 0.003 0.040 2523 Dihedral : 3.750 45.940 2083 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.74 % Allowed : 17.40 % Favored : 80.86 % 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: 2.31 (0.21), residues: 1781 helix: 2.28 (0.15), residues: 1132 sheet: 0.27 (0.64), residues: 59 loop : 0.26 (0.28), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.007 0.001 HIS D 251 PHE 0.009 0.001 PHE D 590 TYR 0.018 0.001 TYR A 199 ARG 0.005 0.000 ARG D 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.75 seconds wall clock time: 56 minutes 20.43 seconds (3380.43 seconds total)