Starting phenix.real_space_refine on Sat Mar 16 12:19:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ev9_28623/03_2024/8ev9_28623_neut_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 9556 2.51 5 N 2387 2.21 5 O 2648 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 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" 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 442": "OD1" <-> "OD2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A 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 ARG 603": "NH1" <-> "NH2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B 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 GLU 272": "OE1" <-> "OE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B ASP 462": "OD1" <-> "OD2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B GLU 524": "OE1" <-> "OE2" 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 582": "OD1" <-> "OD2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 590": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C GLU 198": "OE1" <-> "OE2" 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 GLU 272": "OE1" <-> "OE2" Residue "C PHE 275": "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 GLU 344": "OE1" <-> "OE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C ASP 475": "OD1" <-> "OD2" Residue "C PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 583": "OD1" <-> "OD2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "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 257": "OD1" <-> "OD2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "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 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 GLU 390": "OE1" <-> "OE2" 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 PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D GLU 484": "OE1" <-> "OE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 497": "OD1" <-> "OD2" Residue "D ASP 513": "OD1" <-> "OD2" Residue "D ASP 535": "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 633": "OD1" <-> "OD2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14661 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3631 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 bond proxies already assigned to first conformer: 3695 Chain: "B" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3624 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3681 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "D" Number of atoms: 3591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 bond proxies already assigned to first conformer: 3663 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.46, per 1000 atoms: 0.71 Number of scatterers: 14661 At special positions: 0 Unit cell: (109.56, 109.56, 126.99, 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 2648 8.00 N 2387 7.00 C 9556 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: 5.08 Conformation dependent library (CDL) restraints added in 3.7 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 7 sheets defined 59.8% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 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: 3.827A 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 256 removed outlier: 4.543A pdb=" N LEU A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.680A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 279 " --> pdb=" O ASN A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 279' 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 removed outlier: 3.576A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 488 through 497 Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 592 through 607 Processing helix chain 'B' and resid 167 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 245 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.887A 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: 4.006A pdb=" N LYS B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 479 removed outlier: 5.559A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 581 through 588 removed outlier: 4.237A pdb=" N ALA B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 609 Processing helix chain 'C' and resid 167 through 192 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 195 through 198 No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 200 through 221 Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 271 through 278 removed outlier: 3.705A pdb=" N PHE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.713A 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 456 No H-bonds generated for 'chain 'C' and resid 453 through 456' Processing helix chain 'C' and resid 462 through 477 removed outlier: 5.628A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.564A 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 582 through 585 No H-bonds generated for 'chain 'C' and resid 582 through 585' Processing helix chain 'C' and resid 592 through 608 Processing helix chain 'D' and resid 216 through 241 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 250 through 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: 3.513A pdb=" N TYR D 314 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 315 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE D 317 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.260A 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 490 Processing helix chain 'D' and resid 495 through 501 removed outlier: 4.254A pdb=" N THR D 501 " --> pdb=" O ASP D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 520 removed outlier: 3.654A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 526 removed outlier: 4.323A pdb=" N LYS D 526 " --> pdb=" O ASP D 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 526' Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 621 through 630 removed outlier: 4.701A pdb=" N HIS D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 645 Processing sheet with id= A, first strand: chain 'A' and resid 499 through 502 Processing sheet with id= B, first strand: chain 'B' and resid 499 through 503 Processing sheet with id= C, first strand: chain 'B' and resid 527 through 530 removed outlier: 3.621A pdb=" N ALA B 528 " --> pdb=" O ARG B 569 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 499 through 502 Processing sheet with id= E, first strand: chain 'C' and resid 527 through 530 removed outlier: 3.567A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 560 through 564 Processing sheet with id= G, first strand: chain 'D' and resid 569 through 572 775 hydrogen bonds defined for protein. 2284 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: 3.94 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3951 1.34 - 1.46: 3340 1.46 - 1.58: 7615 1.58 - 1.70: 2 1.70 - 1.82: 105 Bond restraints: 15013 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 3.40e+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 3.39e+02 bond pdb=" C2' PCG B 802 " pdb=" C3' PCG B 802 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " ideal model delta sigma weight residual 1.808 1.532 0.276 2.00e-02 2.50e+03 1.90e+02 ... (remaining 15008 not shown) Histogram of bond angle deviations from ideal: 96.46 - 104.75: 217 104.75 - 113.04: 7942 113.04 - 121.33: 8806 121.33 - 129.61: 3314 129.61 - 137.90: 102 Bond angle restraints: 20381 Sorted by residual: angle pdb=" N ALA C 566 " pdb=" CA ALA C 566 " pdb=" C ALA C 566 " ideal model delta sigma weight residual 108.99 118.23 -9.24 1.57e+00 4.06e-01 3.46e+01 angle pdb=" N THR C 565 " pdb=" CA THR C 565 " pdb=" C THR C 565 " ideal model delta sigma weight residual 113.01 119.38 -6.37 1.20e+00 6.94e-01 2.82e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 112.23 128.13 -15.90 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 128.12 -15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 112.23 128.08 -15.85 3.00e+00 1.11e-01 2.79e+01 ... (remaining 20376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7808 17.99 - 35.98: 865 35.98 - 53.97: 186 53.97 - 71.95: 33 71.95 - 89.94: 16 Dihedral angle restraints: 8908 sinusoidal: 3657 harmonic: 5251 Sorted by residual: dihedral pdb=" CA GLY D 389 " pdb=" C GLY D 389 " pdb=" N GLU D 390 " pdb=" CA GLU D 390 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA APHE A 392 " pdb=" C PHE A 392 " pdb=" N ALA A 393 " pdb=" CA ALA A 393 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLY B 367 " pdb=" C GLY B 367 " pdb=" N GLU B 368 " pdb=" CA GLU B 368 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 8905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2306 0.336 - 0.672: 9 0.672 - 1.008: 0 1.008 - 1.344: 0 1.344 - 1.680: 4 Chirality restraints: 2319 Sorted by residual: 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 7.05e+01 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 7.05e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.04e+01 ... (remaining 2316 not shown) Planarity restraints: 2507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.062 5.00e-02 4.00e+02 9.34e-02 1.39e+01 pdb=" N PRO D 273 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 411 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO D 412 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 412 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 412 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 369 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO A 370 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.036 5.00e-02 4.00e+02 ... (remaining 2504 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 132 2.59 - 3.17: 11651 3.17 - 3.75: 23609 3.75 - 4.32: 31461 4.32 - 4.90: 52710 Nonbonded interactions: 119563 Sorted by model distance: nonbonded pdb=" CG2 ILE D 236 " pdb=" CD PRO D 237 " model vdw 2.017 3.860 nonbonded pdb=" OD1 ASP A 432 " pdb=" N LEU A 433 " model vdw 2.117 2.520 nonbonded pdb=" CB ARG A 564 " pdb=" O1A PCG A 802 " model vdw 2.292 3.440 nonbonded pdb=" CA ARG A 564 " pdb=" O1A PCG A 802 " model vdw 2.315 3.470 nonbonded pdb=" OG1 THR D 605 " pdb=" N2 PCG D 901 " model vdw 2.315 2.520 ... (remaining 119558 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 609 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 609 or resid 801 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 609 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.410 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: 7.180 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 43.200 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.015 0.369 15013 Z= 1.014 Angle : 1.178 15.905 20381 Z= 0.585 Chirality : 0.102 1.680 2319 Planarity : 0.008 0.093 2504 Dihedral : 15.885 89.943 5534 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.44 % Allowed : 15.45 % Favored : 84.12 % 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: -4.23 (0.14), residues: 1766 helix: -2.85 (0.09), residues: 1158 sheet: -2.25 (0.63), residues: 53 loop : -2.25 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 171 HIS 0.006 0.002 HIS D 251 PHE 0.028 0.003 PHE C 301 TYR 0.023 0.003 TYR C 354 ARG 0.014 0.001 ARG D 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7330 (mt-10) REVERT: A 272 GLU cc_start: 0.7121 (mp0) cc_final: 0.6895 (mp0) REVERT: A 414 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.5380 (mp10) REVERT: B 410 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6394 (tmm160) REVERT: B 499 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7339 (ptt-90) REVERT: B 521 ILE cc_start: 0.8566 (mt) cc_final: 0.8191 (mm) REVERT: C 402 MET cc_start: 0.7322 (ttp) cc_final: 0.7060 (ttp) REVERT: C 417 ILE cc_start: 0.8358 (mm) cc_final: 0.8137 (mt) REVERT: C 442 ASP cc_start: 0.7492 (m-30) cc_final: 0.7180 (m-30) REVERT: C 575 ASP cc_start: 0.8418 (t0) cc_final: 0.8195 (t0) REVERT: D 336 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7318 (mt-10) REVERT: D 484 GLU cc_start: 0.6934 (mp0) cc_final: 0.6572 (mm-30) REVERT: D 570 GLN cc_start: 0.7985 (mt0) cc_final: 0.7694 (mt0) outliers start: 7 outliers final: 3 residues processed: 190 average time/residue: 0.2861 time to fit residues: 77.8249 Evaluate side-chains 157 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 456 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 83 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 276 ASN A 299 ASN A 473 HIS B 229 GLN B 241 GLN B 276 ASN B 317 ASN B 398 ASN B 414 GLN C 229 GLN C 248 GLN C 398 ASN C 407 ASN C 414 GLN C 523 ASN D 232 ASN D 339 HIS D 365 HIS D 367 ASN D 426 ASN D 452 GLN ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS D 602 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15013 Z= 0.181 Angle : 0.507 7.961 20381 Z= 0.267 Chirality : 0.039 0.148 2319 Planarity : 0.004 0.074 2504 Dihedral : 5.768 57.627 2084 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 17.45 % Favored : 80.68 % 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 (0.18), residues: 1766 helix: -0.59 (0.13), residues: 1161 sheet: -2.12 (0.62), residues: 53 loop : -1.60 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 171 HIS 0.010 0.001 HIS D 339 PHE 0.017 0.001 PHE D 270 TYR 0.018 0.001 TYR D 252 ARG 0.007 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.6923 (mp0) cc_final: 0.6575 (mp0) REVERT: B 410 ARG cc_start: 0.6668 (mtm110) cc_final: 0.6413 (tmm160) REVERT: B 499 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7105 (ptt-90) REVERT: C 402 MET cc_start: 0.7376 (ttp) cc_final: 0.7143 (ttp) REVERT: C 414 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7535 (mm-40) REVERT: C 418 ASP cc_start: 0.8084 (m-30) cc_final: 0.7635 (m-30) REVERT: C 442 ASP cc_start: 0.7409 (m-30) cc_final: 0.7027 (m-30) REVERT: C 496 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6841 (mm) REVERT: D 353 VAL cc_start: 0.8273 (t) cc_final: 0.7815 (m) REVERT: D 561 MET cc_start: 0.7657 (tpp) cc_final: 0.7268 (tpt) REVERT: D 570 GLN cc_start: 0.7893 (mt0) cc_final: 0.7678 (mt0) outliers start: 30 outliers final: 17 residues processed: 189 average time/residue: 0.2563 time to fit residues: 72.1967 Evaluate side-chains 174 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 456 ARG Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN C 414 GLN C 523 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15013 Z= 0.268 Angle : 0.530 7.936 20381 Z= 0.277 Chirality : 0.041 0.154 2319 Planarity : 0.004 0.064 2504 Dihedral : 5.314 57.103 2080 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.06 % Allowed : 18.95 % Favored : 78.99 % 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: -0.60 (0.19), residues: 1766 helix: 0.25 (0.14), residues: 1161 sheet: -2.75 (0.61), residues: 49 loop : -1.39 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.017 0.001 PHE B 301 TYR 0.021 0.002 TYR A 423 ARG 0.006 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 272 GLU cc_start: 0.6987 (mp0) cc_final: 0.6619 (mp0) REVERT: A 414 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.5737 (mp10) REVERT: A 569 ARG cc_start: 0.7763 (ttp80) cc_final: 0.6433 (ttt180) REVERT: B 410 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6462 (tmm160) REVERT: B 499 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7059 (ptt-90) REVERT: B 507 ASP cc_start: 0.8366 (m-30) cc_final: 0.7784 (m-30) REVERT: C 402 MET cc_start: 0.7457 (ttp) cc_final: 0.7073 (ttp) REVERT: C 414 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7665 (mm-40) REVERT: C 418 ASP cc_start: 0.8155 (m-30) cc_final: 0.7670 (m-30) REVERT: C 442 ASP cc_start: 0.7431 (m-30) cc_final: 0.7051 (m-30) REVERT: C 447 ASN cc_start: 0.8453 (t0) cc_final: 0.8217 (t0) REVERT: D 336 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 428 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6348 (m-80) outliers start: 33 outliers final: 21 residues processed: 189 average time/residue: 0.2503 time to fit residues: 70.8865 Evaluate side-chains 183 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 160 optimal weight: 0.9990 chunk 170 optimal weight: 0.3980 chunk 152 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 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 345 HIS C 414 GLN C 523 ASN D 367 ASN D 453 ASN D 566 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15013 Z= 0.156 Angle : 0.465 7.513 20381 Z= 0.244 Chirality : 0.039 0.139 2319 Planarity : 0.003 0.061 2504 Dihedral : 4.731 57.897 2076 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.06 % Allowed : 19.76 % Favored : 78.17 % 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: 0.14 (0.20), residues: 1766 helix: 0.86 (0.15), residues: 1162 sheet: -2.12 (0.57), residues: 58 loop : -1.22 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 171 HIS 0.002 0.001 HIS D 251 PHE 0.013 0.001 PHE A 192 TYR 0.022 0.001 TYR D 252 ARG 0.005 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.6973 (mp0) cc_final: 0.6627 (mp0) REVERT: A 414 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.5773 (mp10) REVERT: A 569 ARG cc_start: 0.7780 (ttp80) cc_final: 0.6553 (ttt180) REVERT: B 410 ARG cc_start: 0.6664 (mtm110) cc_final: 0.6455 (tmm160) REVERT: C 402 MET cc_start: 0.7434 (ttp) cc_final: 0.7130 (ttp) REVERT: C 414 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7676 (mm-40) REVERT: C 418 ASP cc_start: 0.8151 (m-30) cc_final: 0.7683 (m-30) REVERT: C 442 ASP cc_start: 0.7411 (m-30) cc_final: 0.7012 (m-30) REVERT: C 447 ASN cc_start: 0.8416 (t0) cc_final: 0.8065 (t0) REVERT: C 496 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6879 (mm) REVERT: D 344 ILE cc_start: 0.7218 (tt) cc_final: 0.7013 (pt) REVERT: D 353 VAL cc_start: 0.8270 (t) cc_final: 0.7805 (m) REVERT: D 428 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: D 453 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6923 (t0) outliers start: 33 outliers final: 21 residues processed: 189 average time/residue: 0.2568 time to fit residues: 72.4657 Evaluate side-chains 173 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 453 ASN Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 0.0980 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 453 ASN D 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15013 Z= 0.187 Angle : 0.467 7.424 20381 Z= 0.246 Chirality : 0.040 0.142 2319 Planarity : 0.003 0.059 2504 Dihedral : 4.587 57.703 2076 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.75 % Allowed : 19.89 % Favored : 77.36 % 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: 0.45 (0.20), residues: 1766 helix: 1.10 (0.15), residues: 1161 sheet: -2.02 (0.56), residues: 58 loop : -1.10 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.013 0.001 PHE A 192 TYR 0.018 0.001 TYR D 252 ARG 0.004 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.6993 (mp0) cc_final: 0.6635 (mp0) REVERT: A 414 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.5846 (mp10) REVERT: B 368 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: B 410 ARG cc_start: 0.6698 (mtm110) cc_final: 0.6475 (tmm160) REVERT: C 402 MET cc_start: 0.7459 (ttp) cc_final: 0.7084 (ttp) REVERT: C 414 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7685 (mm-40) REVERT: C 418 ASP cc_start: 0.8138 (m-30) cc_final: 0.7675 (m-30) REVERT: C 442 ASP cc_start: 0.7409 (m-30) cc_final: 0.7005 (m-30) REVERT: C 447 ASN cc_start: 0.8373 (t0) cc_final: 0.7975 (t0) REVERT: C 496 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6872 (mm) REVERT: C 581 LYS cc_start: 0.6701 (tttt) cc_final: 0.6416 (tptm) REVERT: D 336 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7031 (mt-10) REVERT: D 344 ILE cc_start: 0.7251 (tt) cc_final: 0.6987 (pt) REVERT: D 428 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: D 561 MET cc_start: 0.7655 (tpp) cc_final: 0.7394 (tpt) outliers start: 44 outliers final: 30 residues processed: 194 average time/residue: 0.2688 time to fit residues: 77.8129 Evaluate side-chains 187 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 453 ASN Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 164 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 453 ASN D 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15013 Z= 0.164 Angle : 0.452 6.643 20381 Z= 0.238 Chirality : 0.039 0.143 2319 Planarity : 0.003 0.054 2504 Dihedral : 4.315 57.973 2074 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.56 % Allowed : 20.58 % Favored : 76.86 % 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: 0.66 (0.20), residues: 1766 helix: 1.24 (0.15), residues: 1169 sheet: -2.17 (0.54), residues: 64 loop : -0.92 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.016 0.001 PHE D 270 TYR 0.017 0.001 TYR A 423 ARG 0.004 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 272 GLU cc_start: 0.6983 (mp0) cc_final: 0.6629 (mp0) REVERT: A 414 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.5802 (mp10) REVERT: A 569 ARG cc_start: 0.7790 (ttp80) cc_final: 0.6681 (ttt-90) REVERT: B 368 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: B 410 ARG cc_start: 0.6725 (mtm110) cc_final: 0.6464 (tmm160) REVERT: C 402 MET cc_start: 0.7458 (ttp) cc_final: 0.7078 (ttp) REVERT: C 414 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7698 (mm-40) REVERT: C 418 ASP cc_start: 0.8118 (m-30) cc_final: 0.7648 (m-30) REVERT: C 442 ASP cc_start: 0.7422 (m-30) cc_final: 0.7002 (m-30) REVERT: C 447 ASN cc_start: 0.8377 (t0) cc_final: 0.7951 (t0) REVERT: C 496 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6897 (mm) REVERT: C 581 LYS cc_start: 0.6658 (tttt) cc_final: 0.6394 (tptm) REVERT: D 344 ILE cc_start: 0.7258 (tt) cc_final: 0.6964 (pt) REVERT: D 428 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6343 (m-80) REVERT: D 484 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: D 561 MET cc_start: 0.7595 (tpp) cc_final: 0.7291 (tpt) outliers start: 41 outliers final: 27 residues processed: 191 average time/residue: 0.2482 time to fit residues: 71.1659 Evaluate side-chains 184 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 169 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 367 ASN D 426 ASN ** D 453 ASN ** 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: 0.7789 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15013 Z= 0.193 Angle : 0.466 6.578 20381 Z= 0.246 Chirality : 0.040 0.149 2319 Planarity : 0.003 0.051 2504 Dihedral : 4.281 58.598 2074 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.88 % Allowed : 20.83 % Favored : 76.30 % 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: 0.83 (0.20), residues: 1766 helix: 1.34 (0.15), residues: 1165 sheet: -1.97 (0.55), residues: 64 loop : -0.80 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 373 HIS 0.003 0.001 HIS D 251 PHE 0.013 0.001 PHE B 301 TYR 0.017 0.001 TYR A 423 ARG 0.003 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7447 (mp10) REVERT: A 272 GLU cc_start: 0.7042 (mp0) cc_final: 0.6679 (mp0) REVERT: A 414 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.5937 (mp10) REVERT: A 494 LEU cc_start: 0.8204 (mm) cc_final: 0.7892 (mm) REVERT: A 569 ARG cc_start: 0.7781 (ttp80) cc_final: 0.6697 (ttt-90) REVERT: B 368 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 499 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7209 (ptm-80) REVERT: B 507 ASP cc_start: 0.8372 (m-30) cc_final: 0.8061 (m-30) REVERT: C 402 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7071 (ttp) REVERT: C 414 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: C 418 ASP cc_start: 0.8102 (m-30) cc_final: 0.7654 (m-30) REVERT: C 442 ASP cc_start: 0.7418 (m-30) cc_final: 0.7010 (m-30) REVERT: C 447 ASN cc_start: 0.8396 (t0) cc_final: 0.8008 (t0) REVERT: C 496 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6785 (mm) REVERT: C 581 LYS cc_start: 0.6716 (tttt) cc_final: 0.6455 (tptm) REVERT: D 336 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6906 (tt0) REVERT: D 344 ILE cc_start: 0.7274 (tt) cc_final: 0.6932 (pt) REVERT: D 428 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6295 (m-80) REVERT: D 461 ASP cc_start: 0.7008 (t0) cc_final: 0.6731 (t0) REVERT: D 484 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: D 561 MET cc_start: 0.7579 (tpp) cc_final: 0.7298 (tpt) outliers start: 46 outliers final: 29 residues processed: 199 average time/residue: 0.2470 time to fit residues: 73.9118 Evaluate side-chains 196 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 426 ASN ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15013 Z= 0.287 Angle : 0.514 7.168 20381 Z= 0.270 Chirality : 0.042 0.156 2319 Planarity : 0.004 0.052 2504 Dihedral : 4.440 59.071 2074 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.31 % Allowed : 20.58 % Favored : 76.11 % 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: 0.60 (0.20), residues: 1766 helix: 1.14 (0.15), residues: 1167 sheet: -1.89 (0.58), residues: 59 loop : -0.86 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 373 HIS 0.003 0.001 HIS D 251 PHE 0.018 0.001 PHE B 301 TYR 0.022 0.002 TYR A 423 ARG 0.003 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 159 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7931 (mm-40) REVERT: A 272 GLU cc_start: 0.7088 (mp0) cc_final: 0.6688 (mp0) REVERT: A 414 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6100 (mp10) REVERT: A 494 LEU cc_start: 0.8232 (mm) cc_final: 0.7905 (mm) REVERT: B 368 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: B 499 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7216 (ptm-80) REVERT: B 507 ASP cc_start: 0.8399 (m-30) cc_final: 0.8089 (m-30) REVERT: B 607 MET cc_start: 0.6586 (mmp) cc_final: 0.6358 (mmp) REVERT: C 402 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7061 (ttp) REVERT: C 414 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7713 (mm-40) REVERT: C 418 ASP cc_start: 0.8163 (m-30) cc_final: 0.7732 (m-30) REVERT: C 442 ASP cc_start: 0.7472 (m-30) cc_final: 0.7080 (m-30) REVERT: C 447 ASN cc_start: 0.8438 (t0) cc_final: 0.8052 (t0) REVERT: C 496 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6815 (mm) REVERT: C 581 LYS cc_start: 0.6725 (tttt) cc_final: 0.6453 (tptm) REVERT: D 336 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7146 (mt-10) REVERT: D 484 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: D 561 MET cc_start: 0.7622 (tpp) cc_final: 0.7342 (tpt) outliers start: 53 outliers final: 39 residues processed: 196 average time/residue: 0.2457 time to fit residues: 72.8905 Evaluate side-chains 201 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 156 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.0470 chunk 148 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 426 ASN ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15013 Z= 0.141 Angle : 0.449 8.044 20381 Z= 0.236 Chirality : 0.039 0.160 2319 Planarity : 0.003 0.052 2504 Dihedral : 4.210 59.966 2074 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.25 % Allowed : 21.64 % Favored : 76.11 % 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: 1.02 (0.20), residues: 1766 helix: 1.47 (0.15), residues: 1165 sheet: -1.78 (0.58), residues: 64 loop : -0.69 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.014 0.001 PHE D 432 TYR 0.022 0.001 TYR A 423 ARG 0.004 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7871 (mm-40) REVERT: A 272 GLU cc_start: 0.7021 (mp0) cc_final: 0.6646 (mp0) REVERT: A 414 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.5996 (mp10) REVERT: A 494 LEU cc_start: 0.8175 (mm) cc_final: 0.7874 (mm) REVERT: B 368 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: B 499 ARG cc_start: 0.7570 (ttp80) cc_final: 0.6960 (ptp90) REVERT: B 507 ASP cc_start: 0.8365 (m-30) cc_final: 0.7842 (m-30) REVERT: C 402 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7131 (ttp) REVERT: C 442 ASP cc_start: 0.7504 (m-30) cc_final: 0.7100 (m-30) REVERT: C 496 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6793 (mm) REVERT: C 581 LYS cc_start: 0.6685 (tttt) cc_final: 0.6346 (tptm) REVERT: D 344 ILE cc_start: 0.7224 (tt) cc_final: 0.6957 (pt) REVERT: D 428 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: D 461 ASP cc_start: 0.6955 (t0) cc_final: 0.6673 (t0) REVERT: D 484 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: D 561 MET cc_start: 0.7527 (tpp) cc_final: 0.7209 (tpt) outliers start: 36 outliers final: 27 residues processed: 182 average time/residue: 0.2520 time to fit residues: 69.6221 Evaluate side-chains 187 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 426 ASN ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15013 Z= 0.213 Angle : 0.475 6.927 20381 Z= 0.249 Chirality : 0.040 0.159 2319 Planarity : 0.003 0.051 2504 Dihedral : 4.256 59.642 2074 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.13 % Allowed : 21.76 % Favored : 76.11 % 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: 0.99 (0.20), residues: 1766 helix: 1.41 (0.15), residues: 1164 sheet: -1.37 (0.59), residues: 70 loop : -0.66 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.015 0.001 PHE B 301 TYR 0.021 0.001 TYR A 423 ARG 0.003 0.000 ARG A 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7871 (mm-40) REVERT: A 272 GLU cc_start: 0.7037 (mp0) cc_final: 0.6652 (mp0) REVERT: A 414 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6032 (mp10) REVERT: A 494 LEU cc_start: 0.8227 (mm) cc_final: 0.7970 (mm) REVERT: B 368 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: B 499 ARG cc_start: 0.7560 (ttp80) cc_final: 0.6908 (ptm160) REVERT: B 507 ASP cc_start: 0.8394 (m-30) cc_final: 0.8084 (m-30) REVERT: B 607 MET cc_start: 0.6443 (mmp) cc_final: 0.6135 (mmp) REVERT: C 402 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7097 (ttp) REVERT: C 442 ASP cc_start: 0.7438 (m-30) cc_final: 0.7031 (m-30) REVERT: C 447 ASN cc_start: 0.8396 (t0) cc_final: 0.8025 (t0) REVERT: C 496 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6837 (mm) REVERT: C 581 LYS cc_start: 0.6563 (tttt) cc_final: 0.6316 (tptm) REVERT: D 336 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6947 (tt0) REVERT: D 344 ILE cc_start: 0.7270 (tt) cc_final: 0.6938 (pt) REVERT: D 428 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: D 484 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: D 561 MET cc_start: 0.7513 (tpp) cc_final: 0.7136 (tpt) REVERT: D 607 ASN cc_start: 0.7477 (m-40) cc_final: 0.7185 (m-40) outliers start: 34 outliers final: 28 residues processed: 188 average time/residue: 0.2353 time to fit residues: 67.1471 Evaluate side-chains 193 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 40.0000 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.0020 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 143 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN D 426 ASN ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.205801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172638 restraints weight = 25062.043| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.73 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15013 Z= 0.135 Angle : 0.442 6.700 20381 Z= 0.232 Chirality : 0.039 0.159 2319 Planarity : 0.003 0.051 2504 Dihedral : 4.106 59.016 2074 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.88 % Allowed : 22.08 % Favored : 76.05 % 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: 1.24 (0.21), residues: 1766 helix: 1.60 (0.15), residues: 1165 sheet: -1.21 (0.61), residues: 70 loop : -0.56 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 PHE 0.013 0.001 PHE D 432 TYR 0.022 0.001 TYR A 423 ARG 0.004 0.000 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.55 seconds wall clock time: 51 minutes 18.85 seconds (3078.85 seconds total)