Starting phenix.real_space_refine on Fri Feb 16 15:43:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayf_7019/02_2024/6ayf_7019.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayf_7019/02_2024/6ayf_7019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayf_7019/02_2024/6ayf_7019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayf_7019/02_2024/6ayf_7019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayf_7019/02_2024/6ayf_7019.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayf_7019/02_2024/6ayf_7019.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 10360 2.51 5 N 2504 2.21 5 O 2788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 503": "OD1" <-> "OD2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 503": "OD1" <-> "OD2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 503": "OD1" <-> "OD2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "D PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 503": "OD1" <-> "OD2" Residue "D TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15780 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "B" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "C" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "D" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.04, per 1000 atoms: 0.51 Number of scatterers: 15780 At special positions: 0 Unit cell: (108.378, 108.378, 115.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 2788 8.00 N 2504 7.00 C 10360 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 601 " - " ASN A 138 " " NAG A 602 " - " ASN A 172 " " NAG B 601 " - " ASN B 138 " " NAG B 602 " - " ASN B 172 " " NAG C 601 " - " ASN C 138 " " NAG C 602 " - " ASN C 172 " " NAG D 601 " - " ASN D 138 " " NAG D 602 " - " ASN D 172 " Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 2.7 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 64.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.018A pdb=" N PHE A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 3.875A pdb=" N ARG A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 103 removed outlier: 3.506A pdb=" N GLN A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.908A pdb=" N VAL A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 325 removed outlier: 3.608A pdb=" N ALA A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 removed outlier: 3.759A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 365 removed outlier: 3.693A pdb=" N MET A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.564A pdb=" N LEU A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.660A pdb=" N GLN A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Proline residue: A 410 - end of helix removed outlier: 4.075A pdb=" N ARG A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 471 through 490 Processing helix chain 'A' and resid 490 through 514 Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'B' and resid 34 through 46 removed outlier: 4.016A pdb=" N PHE B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.876A pdb=" N ARG B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 103 removed outlier: 3.504A pdb=" N GLN B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 135 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.911A pdb=" N VAL B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 325 removed outlier: 3.605A pdb=" N ALA B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 removed outlier: 3.767A pdb=" N PHE B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 365 removed outlier: 3.704A pdb=" N MET B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.558A pdb=" N LEU B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 399 through 435 removed outlier: 3.655A pdb=" N GLN B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Proline residue: B 410 - end of helix removed outlier: 4.083A pdb=" N ARG B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 456 Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.844A pdb=" N MET B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 490 Processing helix chain 'B' and resid 490 through 514 Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'C' and resid 34 through 46 removed outlier: 4.019A pdb=" N PHE C 44 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.876A pdb=" N ARG C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 57 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 103 removed outlier: 3.505A pdb=" N GLN C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 135 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.908A pdb=" N VAL C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 325 removed outlier: 3.605A pdb=" N ALA C 290 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 323 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 338 removed outlier: 3.763A pdb=" N PHE C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 365 removed outlier: 3.702A pdb=" N MET C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 388 removed outlier: 3.562A pdb=" N LEU C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 394 Processing helix chain 'C' and resid 399 through 435 removed outlier: 3.657A pdb=" N GLN C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Proline residue: C 410 - end of helix removed outlier: 4.082A pdb=" N ARG C 414 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 456 Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 471 through 490 Processing helix chain 'C' and resid 490 through 514 Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'D' and resid 34 through 46 removed outlier: 4.019A pdb=" N PHE D 44 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 removed outlier: 3.874A pdb=" N ARG D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 103 removed outlier: 3.510A pdb=" N GLN D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.914A pdb=" N VAL D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 325 removed outlier: 3.607A pdb=" N ALA D 290 " --> pdb=" O MET D 286 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU D 323 " --> pdb=" O ASN D 319 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS D 324 " --> pdb=" O PHE D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 338 removed outlier: 3.743A pdb=" N PHE D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 365 removed outlier: 3.693A pdb=" N MET D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 388 removed outlier: 3.556A pdb=" N LEU D 376 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 394 Processing helix chain 'D' and resid 399 through 435 removed outlier: 3.659A pdb=" N GLN D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Proline residue: D 410 - end of helix removed outlier: 4.084A pdb=" N ARG D 414 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS D 429 " --> pdb=" O GLY D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 471 through 490 removed outlier: 3.514A pdb=" N ARG D 479 " --> pdb=" O TRP D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 514 Processing helix chain 'D' and resid 519 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 6.930A pdb=" N LEU A 213 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 163 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 158 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 6.930A pdb=" N LEU A 213 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 163 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N HIS A 161 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 182 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR A 163 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 180 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 165 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.501A pdb=" N HIS A 273 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 165 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 180 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR B 163 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU B 182 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS B 161 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR B 163 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 213 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 116 removed outlier: 6.929A pdb=" N LEU B 213 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR B 163 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 158 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 272 through 274 removed outlier: 6.474A pdb=" N HIS B 273 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG C 165 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU C 180 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 163 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU C 182 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS C 161 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR C 163 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU C 213 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 115 through 116 removed outlier: 6.926A pdb=" N LEU C 213 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR C 163 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 158 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 272 through 274 removed outlier: 6.485A pdb=" N HIS C 273 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG D 165 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU D 180 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR D 163 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU D 182 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N HIS D 161 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR D 163 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 213 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 115 through 116 removed outlier: 6.929A pdb=" N LEU D 213 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR D 163 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 158 " --> pdb=" O PHE D 186 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 3078 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: 5.00 Time building geometry restraints manager: 6.56 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: 4798 1.34 - 1.46: 3933 1.46 - 1.58: 7217 1.58 - 1.70: 0 1.70 - 1.82: 200 Bond restraints: 16148 Sorted by residual: bond pdb=" NE ARG D 479 " pdb=" CZ ARG D 479 " ideal model delta sigma weight residual 1.326 1.293 0.033 1.10e-02 8.26e+03 8.81e+00 bond pdb=" C1 NAG D 602 " pdb=" O5 NAG D 602 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.74e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 16143 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.22: 271 106.22 - 113.23: 8745 113.23 - 120.24: 6180 120.24 - 127.25: 6503 127.25 - 134.26: 133 Bond angle restraints: 21832 Sorted by residual: angle pdb=" CA ARG C 479 " pdb=" CB ARG C 479 " pdb=" CG ARG C 479 " ideal model delta sigma weight residual 114.10 106.60 7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" NE ARG D 479 " pdb=" CZ ARG D 479 " pdb=" NH1 ARG D 479 " ideal model delta sigma weight residual 121.50 118.14 3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" C PHE A 415 " pdb=" N CYS A 416 " pdb=" CA CYS A 416 " ideal model delta sigma weight residual 120.54 124.96 -4.42 1.35e+00 5.49e-01 1.07e+01 angle pdb=" NE ARG C 479 " pdb=" CZ ARG C 479 " pdb=" NH1 ARG C 479 " ideal model delta sigma weight residual 121.50 118.27 3.23 1.00e+00 1.00e+00 1.04e+01 angle pdb=" C PHE C 415 " pdb=" N CYS C 416 " pdb=" CA CYS C 416 " ideal model delta sigma weight residual 120.54 124.67 -4.13 1.35e+00 5.49e-01 9.37e+00 ... (remaining 21827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 8052 14.75 - 29.50: 1121 29.50 - 44.26: 342 44.26 - 59.01: 85 59.01 - 73.76: 20 Dihedral angle restraints: 9620 sinusoidal: 3972 harmonic: 5648 Sorted by residual: dihedral pdb=" CA ASP D 333 " pdb=" C ASP D 333 " pdb=" N GLN D 334 " pdb=" CA GLN D 334 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ASP A 333 " pdb=" C ASP A 333 " pdb=" N GLN A 334 " pdb=" CA GLN A 334 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASP B 333 " pdb=" C ASP B 333 " pdb=" N GLN B 334 " pdb=" CA GLN B 334 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 9617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2351 0.094 - 0.187: 133 0.187 - 0.281: 0 0.281 - 0.374: 4 0.374 - 0.468: 4 Chirality restraints: 2492 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 138 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 138 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 2489 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 44 " -0.028 2.00e-02 2.50e+03 2.22e-02 8.63e+00 pdb=" CG PHE B 44 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 44 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 44 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 44 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 44 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE B 44 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 44 " 0.028 2.00e-02 2.50e+03 2.21e-02 8.52e+00 pdb=" CG PHE D 44 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 44 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 44 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 44 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 44 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE D 44 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 44 " 0.028 2.00e-02 2.50e+03 2.19e-02 8.39e+00 pdb=" CG PHE A 44 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 44 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 44 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 44 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 44 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 44 " 0.001 2.00e-02 2.50e+03 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1599 2.75 - 3.29: 16742 3.29 - 3.83: 25708 3.83 - 4.36: 29827 4.36 - 4.90: 51089 Nonbonded interactions: 124965 Sorted by model distance: nonbonded pdb=" OE1 GLN C 66 " pdb=" OG SER C 299 " model vdw 2.213 2.440 nonbonded pdb=" OE1 GLN B 66 " pdb=" OG SER B 299 " model vdw 2.233 2.440 nonbonded pdb=" OE1 GLN D 66 " pdb=" OG SER D 299 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLN A 66 " pdb=" OG SER A 299 " model vdw 2.237 2.440 nonbonded pdb=" CG2 VAL A 329 " pdb=" OE2 GLU A 520 " model vdw 2.242 3.460 ... (remaining 124960 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.860 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 41.030 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.004 0.065 16148 Z= 0.279 Angle : 0.832 8.623 21832 Z= 0.463 Chirality : 0.053 0.468 2492 Planarity : 0.004 0.037 2676 Dihedral : 15.595 73.761 5964 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.81 % Favored : 92.98 % Rotamer: Outliers : 0.11 % Allowed : 22.93 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.14), residues: 1880 helix: -2.94 (0.11), residues: 1084 sheet: -2.19 (0.23), residues: 260 loop : -2.80 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 475 HIS 0.005 0.001 HIS B 144 PHE 0.046 0.003 PHE B 44 TYR 0.019 0.002 TYR C 426 ARG 0.022 0.001 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 498 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8412 (tpt170) cc_final: 0.7886 (ttm110) REVERT: A 58 ARG cc_start: 0.6961 (ttt90) cc_final: 0.6116 (tpt170) REVERT: A 61 TRP cc_start: 0.7531 (m100) cc_final: 0.7231 (m100) REVERT: A 164 LYS cc_start: 0.8391 (tttt) cc_final: 0.5549 (ttpt) REVERT: A 165 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7175 (ttp80) REVERT: A 180 GLU cc_start: 0.8180 (tt0) cc_final: 0.7358 (mm-30) REVERT: A 289 ASP cc_start: 0.8529 (m-30) cc_final: 0.7966 (m-30) REVERT: A 298 VAL cc_start: 0.8350 (t) cc_final: 0.8081 (t) REVERT: A 307 VAL cc_start: 0.9346 (t) cc_final: 0.9121 (t) REVERT: A 314 GLN cc_start: 0.8938 (pt0) cc_final: 0.8513 (tm-30) REVERT: A 335 MET cc_start: 0.8506 (mmm) cc_final: 0.8195 (mmp) REVERT: A 337 PHE cc_start: 0.8205 (m-80) cc_final: 0.7362 (m-80) REVERT: A 344 MET cc_start: 0.8642 (ttm) cc_final: 0.8415 (ttm) REVERT: A 345 ILE cc_start: 0.9277 (mm) cc_final: 0.8966 (mm) REVERT: A 460 MET cc_start: 0.9074 (ttm) cc_final: 0.8785 (ttm) REVERT: A 470 LYS cc_start: 0.8673 (tttt) cc_final: 0.8461 (mmtt) REVERT: A 503 ASP cc_start: 0.8365 (t70) cc_final: 0.7846 (m-30) REVERT: A 522 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7356 (ttm110) REVERT: B 40 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7781 (ttm110) REVERT: B 58 ARG cc_start: 0.6949 (ttt90) cc_final: 0.6555 (tpt170) REVERT: B 61 TRP cc_start: 0.7523 (m100) cc_final: 0.7249 (m-10) REVERT: B 165 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7086 (ttp80) REVERT: B 180 GLU cc_start: 0.8137 (tt0) cc_final: 0.7350 (mm-30) REVERT: B 208 LEU cc_start: 0.8580 (mp) cc_final: 0.8309 (mt) REVERT: B 244 THR cc_start: 0.8870 (p) cc_final: 0.7587 (m) REVERT: B 261 ASP cc_start: 0.8634 (m-30) cc_final: 0.8417 (p0) REVERT: B 266 ILE cc_start: 0.9114 (mt) cc_final: 0.8866 (mp) REVERT: B 298 VAL cc_start: 0.8404 (t) cc_final: 0.8123 (t) REVERT: B 307 VAL cc_start: 0.9261 (t) cc_final: 0.9060 (t) REVERT: B 311 LEU cc_start: 0.8987 (mt) cc_final: 0.8617 (tp) REVERT: B 314 GLN cc_start: 0.8803 (pt0) cc_final: 0.8280 (tm-30) REVERT: B 335 MET cc_start: 0.8498 (mmm) cc_final: 0.8185 (mmp) REVERT: B 337 PHE cc_start: 0.8280 (m-80) cc_final: 0.7425 (m-80) REVERT: B 345 ILE cc_start: 0.9199 (mm) cc_final: 0.8942 (mm) REVERT: B 385 TRP cc_start: 0.9280 (m100) cc_final: 0.8996 (m100) REVERT: B 421 MET cc_start: 0.9319 (mmp) cc_final: 0.9009 (mmm) REVERT: B 460 MET cc_start: 0.9103 (ttm) cc_final: 0.8789 (ttm) REVERT: B 479 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7921 (ttm170) REVERT: B 503 ASP cc_start: 0.8316 (t70) cc_final: 0.7785 (m-30) REVERT: B 513 GLN cc_start: 0.8557 (tt0) cc_final: 0.8313 (mt0) REVERT: C 164 LYS cc_start: 0.8339 (tttt) cc_final: 0.5345 (ttpt) REVERT: C 165 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7361 (ttp80) REVERT: C 180 GLU cc_start: 0.8245 (tt0) cc_final: 0.7573 (mm-30) REVERT: C 266 ILE cc_start: 0.9096 (mt) cc_final: 0.8859 (mp) REVERT: C 286 MET cc_start: 0.9013 (mmm) cc_final: 0.8771 (tpp) REVERT: C 298 VAL cc_start: 0.8721 (t) cc_final: 0.8463 (t) REVERT: C 314 GLN cc_start: 0.9046 (pt0) cc_final: 0.8471 (tm-30) REVERT: C 317 PHE cc_start: 0.8398 (t80) cc_final: 0.7929 (t80) REVERT: C 335 MET cc_start: 0.8431 (mmm) cc_final: 0.8175 (mmp) REVERT: C 337 PHE cc_start: 0.7963 (m-80) cc_final: 0.7320 (m-80) REVERT: C 345 ILE cc_start: 0.9199 (mm) cc_final: 0.8798 (mm) REVERT: C 421 MET cc_start: 0.9381 (mmp) cc_final: 0.9134 (mmm) REVERT: C 460 MET cc_start: 0.8940 (ttm) cc_final: 0.8256 (ttm) REVERT: C 470 LYS cc_start: 0.9026 (tttt) cc_final: 0.8817 (mmtt) REVERT: C 479 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8256 (tpp80) REVERT: C 503 ASP cc_start: 0.8272 (t70) cc_final: 0.8009 (m-30) REVERT: C 511 TYR cc_start: 0.7997 (m-10) cc_final: 0.7796 (m-10) REVERT: D 50 CYS cc_start: 0.7090 (m) cc_final: 0.6781 (t) REVERT: D 126 LEU cc_start: 0.9181 (mt) cc_final: 0.8957 (tp) REVERT: D 164 LYS cc_start: 0.8341 (tttt) cc_final: 0.4823 (ttpt) REVERT: D 165 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7275 (ttp80) REVERT: D 180 GLU cc_start: 0.8248 (tt0) cc_final: 0.7359 (mm-30) REVERT: D 266 ILE cc_start: 0.9027 (mt) cc_final: 0.8734 (mp) REVERT: D 289 ASP cc_start: 0.8661 (m-30) cc_final: 0.8065 (m-30) REVERT: D 298 VAL cc_start: 0.8503 (t) cc_final: 0.8254 (t) REVERT: D 314 GLN cc_start: 0.8977 (pt0) cc_final: 0.8475 (tm-30) REVERT: D 317 PHE cc_start: 0.8213 (t80) cc_final: 0.7667 (t80) REVERT: D 337 PHE cc_start: 0.7856 (m-80) cc_final: 0.7123 (m-80) REVERT: D 344 MET cc_start: 0.8750 (ttm) cc_final: 0.8535 (ttm) REVERT: D 345 ILE cc_start: 0.9187 (mm) cc_final: 0.8765 (mm) REVERT: D 460 MET cc_start: 0.8813 (ttm) cc_final: 0.8153 (mtt) REVERT: D 467 MET cc_start: 0.9201 (mmm) cc_final: 0.8726 (mmm) REVERT: D 503 ASP cc_start: 0.8279 (t70) cc_final: 0.7993 (m-30) outliers start: 2 outliers final: 0 residues processed: 500 average time/residue: 0.2758 time to fit residues: 201.2161 Evaluate side-chains 331 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 329 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 479 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN A 339 ASN A 445 ASN B 339 ASN B 445 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 339 ASN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 339 ASN D 445 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16148 Z= 0.221 Angle : 0.627 6.878 21832 Z= 0.341 Chirality : 0.044 0.256 2492 Planarity : 0.004 0.041 2676 Dihedral : 6.316 42.187 2236 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 6.44 % Allowed : 20.52 % Favored : 73.05 % 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: -1.14 (0.18), residues: 1880 helix: 0.04 (0.14), residues: 1116 sheet: -1.29 (0.27), residues: 276 loop : -2.00 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 431 HIS 0.004 0.001 HIS B 252 PHE 0.024 0.002 PHE A 497 TYR 0.013 0.001 TYR B 398 ARG 0.005 0.001 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 338 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7212 (tpt) cc_final: 0.6841 (tpp) REVERT: A 147 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6476 (mt-10) REVERT: A 180 GLU cc_start: 0.7652 (tt0) cc_final: 0.7376 (mm-30) REVERT: A 181 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 232 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.7005 (m-70) REVERT: A 240 ASP cc_start: 0.8237 (t0) cc_final: 0.7872 (t0) REVERT: A 283 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.7870 (p90) REVERT: A 298 VAL cc_start: 0.8776 (t) cc_final: 0.8456 (t) REVERT: A 314 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: A 317 PHE cc_start: 0.7914 (t80) cc_final: 0.7493 (t80) REVERT: A 335 MET cc_start: 0.7945 (mmm) cc_final: 0.7650 (mmp) REVERT: A 337 PHE cc_start: 0.7806 (m-80) cc_final: 0.7548 (m-80) REVERT: A 345 ILE cc_start: 0.9101 (mm) cc_final: 0.8751 (mm) REVERT: A 389 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9308 (mm) REVERT: A 460 MET cc_start: 0.9041 (ttm) cc_final: 0.8550 (ttm) REVERT: A 470 LYS cc_start: 0.8673 (tttt) cc_final: 0.8441 (mmtt) REVERT: B 47 MET cc_start: 0.7063 (tpp) cc_final: 0.6788 (tpp) REVERT: B 56 ARG cc_start: 0.7512 (ttt-90) cc_final: 0.7115 (ttp80) REVERT: B 180 GLU cc_start: 0.7627 (tt0) cc_final: 0.7191 (mm-30) REVERT: B 181 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 208 LEU cc_start: 0.8417 (mp) cc_final: 0.8190 (mt) REVERT: B 213 LEU cc_start: 0.9410 (tt) cc_final: 0.9143 (tp) REVERT: B 232 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7205 (m90) REVERT: B 271 ASP cc_start: 0.7974 (t0) cc_final: 0.7658 (t0) REVERT: B 283 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.7948 (p90) REVERT: B 314 GLN cc_start: 0.8729 (pt0) cc_final: 0.8421 (tm-30) REVERT: B 317 PHE cc_start: 0.8300 (t80) cc_final: 0.7884 (t80) REVERT: B 335 MET cc_start: 0.7886 (mmm) cc_final: 0.7628 (mmp) REVERT: B 337 PHE cc_start: 0.7883 (m-80) cc_final: 0.7616 (m-80) REVERT: B 341 TRP cc_start: 0.8560 (m100) cc_final: 0.8018 (m100) REVERT: B 418 CYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8632 (m) REVERT: B 460 MET cc_start: 0.9134 (ttm) cc_final: 0.8827 (ttp) REVERT: B 479 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8460 (mmt-90) REVERT: B 513 GLN cc_start: 0.8663 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 516 PHE cc_start: 0.7163 (m-80) cc_final: 0.6912 (m-80) REVERT: C 40 ARG cc_start: 0.8459 (tpt170) cc_final: 0.7835 (ttm110) REVERT: C 47 MET cc_start: 0.7586 (tpt) cc_final: 0.7102 (tpp) REVERT: C 56 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.6938 (ttp80) REVERT: C 180 GLU cc_start: 0.7462 (tt0) cc_final: 0.7248 (mm-30) REVERT: C 206 LEU cc_start: 0.8075 (tp) cc_final: 0.7868 (tp) REVERT: C 232 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7082 (m90) REVERT: C 271 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7164 (p0) REVERT: C 279 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7388 (tp-100) REVERT: C 298 VAL cc_start: 0.8995 (t) cc_final: 0.8636 (t) REVERT: C 317 PHE cc_start: 0.8068 (t80) cc_final: 0.7598 (t80) REVERT: C 319 ASN cc_start: 0.8649 (m110) cc_final: 0.8215 (p0) REVERT: C 335 MET cc_start: 0.8043 (mmm) cc_final: 0.7776 (mmp) REVERT: C 345 ILE cc_start: 0.8842 (mm) cc_final: 0.8338 (mm) REVERT: C 460 MET cc_start: 0.9056 (ttm) cc_final: 0.8783 (ttm) REVERT: C 479 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8385 (mmt-90) REVERT: D 47 MET cc_start: 0.7231 (tpt) cc_final: 0.6667 (tpp) REVERT: D 126 LEU cc_start: 0.9207 (mt) cc_final: 0.8768 (tt) REVERT: D 147 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6558 (mt-10) REVERT: D 232 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.7111 (m-70) REVERT: D 240 ASP cc_start: 0.8263 (t0) cc_final: 0.7962 (t0) REVERT: D 271 ASP cc_start: 0.8012 (t0) cc_final: 0.7673 (t0) REVERT: D 298 VAL cc_start: 0.8758 (t) cc_final: 0.8371 (t) REVERT: D 317 PHE cc_start: 0.8058 (t80) cc_final: 0.7462 (t80) REVERT: D 344 MET cc_start: 0.8652 (ttm) cc_final: 0.8347 (ttp) REVERT: D 345 ILE cc_start: 0.8871 (mm) cc_final: 0.8536 (mm) REVERT: D 460 MET cc_start: 0.8965 (ttm) cc_final: 0.8417 (ttm) REVERT: D 479 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8555 (mmt-90) outliers start: 112 outliers final: 52 residues processed: 423 average time/residue: 0.2786 time to fit residues: 174.5236 Evaluate side-chains 349 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 282 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 0.2980 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 144 HIS ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16148 Z= 0.363 Angle : 0.640 8.653 21832 Z= 0.347 Chirality : 0.044 0.220 2492 Planarity : 0.004 0.041 2676 Dihedral : 6.216 43.912 2236 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 6.72 % Allowed : 20.63 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1880 helix: 0.90 (0.15), residues: 1116 sheet: -1.15 (0.28), residues: 280 loop : -1.93 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 272 HIS 0.004 0.001 HIS C 144 PHE 0.025 0.002 PHE A 497 TYR 0.018 0.002 TYR A 481 ARG 0.013 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 294 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7589 (tpt) cc_final: 0.6983 (tpp) REVERT: A 147 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6882 (mt-10) REVERT: A 180 GLU cc_start: 0.7517 (tt0) cc_final: 0.7151 (mm-30) REVERT: A 232 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6953 (m-70) REVERT: A 283 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7938 (p90) REVERT: A 314 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: A 317 PHE cc_start: 0.7983 (t80) cc_final: 0.7502 (t80) REVERT: A 319 ASN cc_start: 0.8710 (m110) cc_final: 0.8385 (p0) REVERT: A 337 PHE cc_start: 0.7952 (m-80) cc_final: 0.7456 (m-80) REVERT: A 467 MET cc_start: 0.9228 (mmm) cc_final: 0.8952 (mmm) REVERT: A 470 LYS cc_start: 0.8865 (tttt) cc_final: 0.8591 (mmtt) REVERT: B 47 MET cc_start: 0.7271 (tpp) cc_final: 0.7050 (tpp) REVERT: B 56 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.6955 (tmm160) REVERT: B 181 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8510 (mp) REVERT: B 232 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7087 (m90) REVERT: B 271 ASP cc_start: 0.7849 (t0) cc_final: 0.7567 (t70) REVERT: B 283 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7874 (p90) REVERT: B 317 PHE cc_start: 0.8389 (t80) cc_final: 0.7979 (t80) REVERT: B 335 MET cc_start: 0.8003 (mmm) cc_final: 0.7682 (mmp) REVERT: B 337 PHE cc_start: 0.8098 (m-80) cc_final: 0.7523 (m-80) REVERT: B 418 CYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8676 (m) REVERT: B 479 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8525 (mmt-90) REVERT: C 47 MET cc_start: 0.7790 (tpt) cc_final: 0.7354 (tpp) REVERT: C 56 ARG cc_start: 0.7681 (ttt-90) cc_final: 0.7009 (ttp80) REVERT: C 232 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7156 (m90) REVERT: C 314 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 317 PHE cc_start: 0.8098 (t80) cc_final: 0.7817 (t80) REVERT: C 319 ASN cc_start: 0.8582 (m110) cc_final: 0.8213 (p0) REVERT: C 335 MET cc_start: 0.8020 (mmm) cc_final: 0.7693 (mmp) REVERT: C 345 ILE cc_start: 0.8846 (mm) cc_final: 0.8618 (mm) REVERT: C 432 ILE cc_start: 0.8750 (tp) cc_final: 0.8534 (tp) REVERT: C 467 MET cc_start: 0.9293 (mmm) cc_final: 0.8934 (mmm) REVERT: C 479 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8489 (mmt-90) REVERT: D 38 MET cc_start: 0.8086 (tmm) cc_final: 0.7477 (tmm) REVERT: D 47 MET cc_start: 0.7496 (tpt) cc_final: 0.7019 (tpp) REVERT: D 126 LEU cc_start: 0.9083 (mt) cc_final: 0.8835 (tp) REVERT: D 232 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.7047 (m-70) REVERT: D 271 ASP cc_start: 0.7635 (t0) cc_final: 0.7411 (t0) REVERT: D 315 GLN cc_start: 0.8603 (mm110) cc_final: 0.8059 (mm-40) REVERT: D 317 PHE cc_start: 0.8090 (t80) cc_final: 0.7590 (t80) REVERT: D 319 ASN cc_start: 0.8681 (m110) cc_final: 0.8326 (p0) REVERT: D 344 MET cc_start: 0.8671 (ttm) cc_final: 0.8405 (ttp) REVERT: D 421 MET cc_start: 0.9330 (mmp) cc_final: 0.9104 (mmm) outliers start: 117 outliers final: 70 residues processed: 384 average time/residue: 0.2591 time to fit residues: 152.0022 Evaluate side-chains 337 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 256 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 504 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.0020 chunk 128 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 281 ASN D 100 HIS D 314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16148 Z= 0.153 Angle : 0.518 9.314 21832 Z= 0.280 Chirality : 0.039 0.214 2492 Planarity : 0.003 0.077 2676 Dihedral : 5.598 39.903 2236 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.06 % Allowed : 22.53 % Favored : 72.41 % 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: 0.54 (0.19), residues: 1880 helix: 1.60 (0.15), residues: 1120 sheet: -0.92 (0.29), residues: 280 loop : -1.79 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 475 HIS 0.003 0.001 HIS C 252 PHE 0.017 0.001 PHE A 497 TYR 0.014 0.001 TYR D 481 ARG 0.005 0.000 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 304 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7542 (tpt) cc_final: 0.7018 (tpp) REVERT: A 65 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 232 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.6981 (m-70) REVERT: A 283 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.7449 (p90) REVERT: A 317 PHE cc_start: 0.7974 (t80) cc_final: 0.7647 (t80) REVERT: A 319 ASN cc_start: 0.8645 (m110) cc_final: 0.8282 (p0) REVERT: A 337 PHE cc_start: 0.7990 (m-80) cc_final: 0.7398 (m-80) REVERT: A 344 MET cc_start: 0.8559 (ttm) cc_final: 0.8174 (ttp) REVERT: A 367 LEU cc_start: 0.8244 (mp) cc_final: 0.8038 (mm) REVERT: A 467 MET cc_start: 0.9180 (mmm) cc_final: 0.8871 (mmm) REVERT: A 470 LYS cc_start: 0.8761 (tttt) cc_final: 0.8483 (mmtm) REVERT: A 476 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8926 (tt) REVERT: B 47 MET cc_start: 0.7393 (tpp) cc_final: 0.7157 (tpp) REVERT: B 56 ARG cc_start: 0.7573 (ttt-90) cc_final: 0.6780 (tmm160) REVERT: B 65 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 213 LEU cc_start: 0.9291 (tt) cc_final: 0.8939 (tp) REVERT: B 232 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7073 (m90) REVERT: B 271 ASP cc_start: 0.7742 (t0) cc_final: 0.7509 (t0) REVERT: B 283 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.7542 (p90) REVERT: B 317 PHE cc_start: 0.7855 (t80) cc_final: 0.7617 (t80) REVERT: B 319 ASN cc_start: 0.8520 (m110) cc_final: 0.8274 (p0) REVERT: B 335 MET cc_start: 0.7596 (mmm) cc_final: 0.7297 (mmp) REVERT: B 418 CYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8723 (m) REVERT: B 476 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9012 (tt) REVERT: B 479 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8393 (mmt-90) REVERT: C 47 MET cc_start: 0.7766 (tpt) cc_final: 0.7296 (tpp) REVERT: C 56 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.6921 (ttp80) REVERT: C 65 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8636 (tt) REVERT: C 125 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: C 213 LEU cc_start: 0.9305 (tt) cc_final: 0.8982 (tp) REVERT: C 232 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7187 (m-70) REVERT: C 314 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8754 (tm-30) REVERT: C 315 GLN cc_start: 0.8698 (mm110) cc_final: 0.8416 (mm-40) REVERT: C 317 PHE cc_start: 0.7947 (t80) cc_final: 0.7717 (t80) REVERT: C 319 ASN cc_start: 0.8468 (m110) cc_final: 0.8194 (p0) REVERT: C 335 MET cc_start: 0.8149 (mmm) cc_final: 0.7908 (mmp) REVERT: C 432 ILE cc_start: 0.8414 (tp) cc_final: 0.8210 (tp) REVERT: C 479 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8460 (mmt-90) REVERT: D 38 MET cc_start: 0.8041 (tmm) cc_final: 0.7447 (tmm) REVERT: D 45 PHE cc_start: 0.8045 (t80) cc_final: 0.7782 (t80) REVERT: D 47 MET cc_start: 0.7593 (tpt) cc_final: 0.7103 (tpp) REVERT: D 147 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6883 (mt-10) REVERT: D 232 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.7063 (m-70) REVERT: D 271 ASP cc_start: 0.7166 (t0) cc_final: 0.6930 (t0) REVERT: D 317 PHE cc_start: 0.7814 (t80) cc_final: 0.7569 (t80) REVERT: D 319 ASN cc_start: 0.8732 (m110) cc_final: 0.8364 (p0) REVERT: D 344 MET cc_start: 0.8761 (ttm) cc_final: 0.8511 (ttp) REVERT: D 367 LEU cc_start: 0.8156 (mp) cc_final: 0.7947 (mm) REVERT: D 421 MET cc_start: 0.9278 (mmp) cc_final: 0.8940 (mmm) REVERT: D 476 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9081 (tt) REVERT: D 479 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8337 (mmt90) outliers start: 88 outliers final: 49 residues processed: 371 average time/residue: 0.2399 time to fit residues: 136.0040 Evaluate side-chains 325 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 259 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN B 100 HIS C 100 HIS C 125 GLN C 281 ASN C 324 HIS D 125 GLN D 281 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16148 Z= 0.283 Angle : 0.589 9.501 21832 Z= 0.310 Chirality : 0.041 0.193 2492 Planarity : 0.003 0.042 2676 Dihedral : 5.647 41.653 2236 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.69 % Allowed : 23.74 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1880 helix: 1.64 (0.15), residues: 1120 sheet: -0.91 (0.28), residues: 276 loop : -1.77 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 272 HIS 0.002 0.001 HIS C 100 PHE 0.020 0.002 PHE A 497 TYR 0.017 0.002 TYR A 481 ARG 0.004 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 267 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7751 (tpt) cc_final: 0.7226 (tpp) REVERT: A 119 GLN cc_start: 0.8401 (pt0) cc_final: 0.8195 (pt0) REVERT: A 147 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 232 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.6930 (m-70) REVERT: A 283 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7682 (p90) REVERT: A 317 PHE cc_start: 0.8002 (t80) cc_final: 0.7549 (t80) REVERT: A 319 ASN cc_start: 0.8591 (m110) cc_final: 0.8317 (p0) REVERT: A 344 MET cc_start: 0.8575 (ttm) cc_final: 0.8370 (ttm) REVERT: A 467 MET cc_start: 0.9195 (mmm) cc_final: 0.8893 (mmm) REVERT: A 470 LYS cc_start: 0.8864 (tttt) cc_final: 0.8588 (mmtt) REVERT: B 38 MET cc_start: 0.7930 (tmm) cc_final: 0.7724 (ppp) REVERT: B 47 MET cc_start: 0.7485 (tpp) cc_final: 0.7231 (tpp) REVERT: B 119 GLN cc_start: 0.8391 (pt0) cc_final: 0.8103 (pt0) REVERT: B 232 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7026 (m90) REVERT: B 271 ASP cc_start: 0.7438 (t0) cc_final: 0.7205 (t0) REVERT: B 283 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.7728 (p90) REVERT: B 319 ASN cc_start: 0.8533 (m110) cc_final: 0.8302 (p0) REVERT: B 335 MET cc_start: 0.7691 (mmm) cc_final: 0.7354 (mmp) REVERT: B 363 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 418 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8526 (m) REVERT: B 476 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8994 (tt) REVERT: B 479 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8471 (mmt-90) REVERT: C 44 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5987 (p90) REVERT: C 47 MET cc_start: 0.7901 (tpt) cc_final: 0.7357 (tpp) REVERT: C 56 ARG cc_start: 0.7677 (ttt-90) cc_final: 0.6940 (ttp80) REVERT: C 218 LEU cc_start: 0.9335 (mt) cc_final: 0.9100 (mt) REVERT: C 232 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7083 (m-70) REVERT: C 314 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 315 GLN cc_start: 0.8712 (mm110) cc_final: 0.8341 (mm-40) REVERT: C 317 PHE cc_start: 0.7964 (t80) cc_final: 0.7705 (t80) REVERT: C 319 ASN cc_start: 0.8515 (m110) cc_final: 0.8186 (p0) REVERT: C 335 MET cc_start: 0.8125 (mmm) cc_final: 0.7889 (mmp) REVERT: C 367 LEU cc_start: 0.8071 (mp) cc_final: 0.7861 (mp) REVERT: C 479 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8488 (mmt-90) REVERT: D 38 MET cc_start: 0.8208 (tmm) cc_final: 0.7914 (tmm) REVERT: D 47 MET cc_start: 0.7657 (tpt) cc_final: 0.7123 (tpp) REVERT: D 177 ILE cc_start: 0.7432 (mt) cc_final: 0.7177 (pt) REVERT: D 232 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.7013 (m-70) REVERT: D 315 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8409 (mm-40) REVERT: D 317 PHE cc_start: 0.7873 (t80) cc_final: 0.7582 (t80) REVERT: D 319 ASN cc_start: 0.8726 (m110) cc_final: 0.8497 (p0) REVERT: D 421 MET cc_start: 0.9273 (mmp) cc_final: 0.9055 (mmp) REVERT: D 476 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9089 (tt) outliers start: 99 outliers final: 70 residues processed: 346 average time/residue: 0.2570 time to fit residues: 134.7173 Evaluate side-chains 333 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 251 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 508 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 7.9990 chunk 163 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN C 125 GLN C 281 ASN D 125 GLN D 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16148 Z= 0.186 Angle : 0.543 8.850 21832 Z= 0.283 Chirality : 0.040 0.199 2492 Planarity : 0.003 0.042 2676 Dihedral : 5.435 42.578 2236 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.40 % Allowed : 23.28 % Favored : 71.32 % 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: 0.85 (0.19), residues: 1880 helix: 1.86 (0.15), residues: 1120 sheet: -0.84 (0.28), residues: 276 loop : -1.67 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 272 HIS 0.003 0.001 HIS C 252 PHE 0.018 0.002 PHE A 497 TYR 0.014 0.001 TYR A 481 ARG 0.006 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 273 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7764 (tpt) cc_final: 0.7258 (tpp) REVERT: A 232 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6942 (m-70) REVERT: A 283 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.7759 (p90) REVERT: A 317 PHE cc_start: 0.7918 (t80) cc_final: 0.7632 (t80) REVERT: A 319 ASN cc_start: 0.8592 (m110) cc_final: 0.8283 (p0) REVERT: A 344 MET cc_start: 0.8494 (ttm) cc_final: 0.8274 (ttm) REVERT: A 467 MET cc_start: 0.9165 (mmm) cc_final: 0.8857 (mmm) REVERT: B 44 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6051 (p90) REVERT: B 47 MET cc_start: 0.7476 (tpp) cc_final: 0.7224 (tpp) REVERT: B 56 ARG cc_start: 0.7859 (ttt-90) cc_final: 0.7112 (tmm160) REVERT: B 232 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7030 (m90) REVERT: B 271 ASP cc_start: 0.7444 (t0) cc_final: 0.7193 (t0) REVERT: B 283 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7749 (p90) REVERT: B 319 ASN cc_start: 0.8476 (m110) cc_final: 0.8131 (p0) REVERT: B 335 MET cc_start: 0.7669 (mmm) cc_final: 0.7335 (mmp) REVERT: B 363 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 418 CYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8654 (m) REVERT: B 476 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 479 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8453 (mmt-90) REVERT: C 44 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6022 (p90) REVERT: C 47 MET cc_start: 0.7828 (tpt) cc_final: 0.7293 (tpp) REVERT: C 56 ARG cc_start: 0.7650 (ttt-90) cc_final: 0.6878 (tmm160) REVERT: C 72 MET cc_start: 0.8806 (mmp) cc_final: 0.8578 (mmm) REVERT: C 177 ILE cc_start: 0.7594 (mt) cc_final: 0.7287 (mm) REVERT: C 232 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.7071 (m-70) REVERT: C 315 GLN cc_start: 0.8734 (mm110) cc_final: 0.8359 (mm-40) REVERT: C 317 PHE cc_start: 0.7917 (t80) cc_final: 0.7685 (t80) REVERT: C 319 ASN cc_start: 0.8465 (m110) cc_final: 0.8174 (p0) REVERT: C 335 MET cc_start: 0.8183 (mmm) cc_final: 0.7947 (mmp) REVERT: C 390 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8102 (ttp-170) REVERT: C 479 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8469 (mmt-90) REVERT: D 38 MET cc_start: 0.8267 (tmm) cc_final: 0.7980 (tmm) REVERT: D 47 MET cc_start: 0.7681 (tpt) cc_final: 0.7103 (tpp) REVERT: D 177 ILE cc_start: 0.7557 (mt) cc_final: 0.7307 (mm) REVERT: D 232 HIS cc_start: 0.7404 (OUTLIER) cc_final: 0.7009 (m-70) REVERT: D 315 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8284 (mm-40) REVERT: D 317 PHE cc_start: 0.7848 (t80) cc_final: 0.7584 (t80) REVERT: D 319 ASN cc_start: 0.8668 (m110) cc_final: 0.8463 (p0) REVERT: D 390 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8112 (ttp-110) REVERT: D 476 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9044 (tt) outliers start: 94 outliers final: 64 residues processed: 346 average time/residue: 0.2560 time to fit residues: 133.1453 Evaluate side-chains 335 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 256 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 101 optimal weight: 0.0570 chunk 181 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN C 125 GLN C 281 ASN D 125 GLN D 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16148 Z= 0.199 Angle : 0.550 10.200 21832 Z= 0.285 Chirality : 0.040 0.200 2492 Planarity : 0.003 0.043 2676 Dihedral : 5.366 42.589 2236 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.80 % Allowed : 23.39 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 1880 helix: 1.95 (0.15), residues: 1120 sheet: -0.81 (0.28), residues: 276 loop : -1.62 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 272 HIS 0.002 0.001 HIS C 252 PHE 0.018 0.002 PHE A 497 TYR 0.015 0.001 TYR A 481 ARG 0.006 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 276 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5936 (p90) REVERT: A 47 MET cc_start: 0.7733 (tpt) cc_final: 0.7207 (tpp) REVERT: A 232 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.7031 (m-70) REVERT: A 283 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7785 (p90) REVERT: A 317 PHE cc_start: 0.7898 (t80) cc_final: 0.7608 (t80) REVERT: A 319 ASN cc_start: 0.8628 (m110) cc_final: 0.8369 (p0) REVERT: A 344 MET cc_start: 0.8484 (ttm) cc_final: 0.8104 (ttp) REVERT: A 467 MET cc_start: 0.9168 (mmm) cc_final: 0.8864 (mmm) REVERT: B 38 MET cc_start: 0.7734 (tmm) cc_final: 0.7490 (ppp) REVERT: B 44 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6055 (p90) REVERT: B 47 MET cc_start: 0.7484 (tpp) cc_final: 0.7224 (tpp) REVERT: B 56 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7075 (tmm160) REVERT: B 232 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7054 (m-70) REVERT: B 271 ASP cc_start: 0.7319 (t0) cc_final: 0.7078 (t0) REVERT: B 283 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7840 (p90) REVERT: B 286 MET cc_start: 0.8829 (mmm) cc_final: 0.8517 (tpp) REVERT: B 319 ASN cc_start: 0.8577 (m110) cc_final: 0.8253 (p0) REVERT: B 335 MET cc_start: 0.7688 (mmm) cc_final: 0.7354 (mmp) REVERT: B 363 GLN cc_start: 0.8625 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 418 CYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8634 (m) REVERT: B 476 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8958 (tt) REVERT: B 479 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8433 (mmt-90) REVERT: C 44 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5939 (p90) REVERT: C 47 MET cc_start: 0.7897 (tpt) cc_final: 0.7410 (tpp) REVERT: C 72 MET cc_start: 0.8798 (mmp) cc_final: 0.8579 (mmm) REVERT: C 177 ILE cc_start: 0.7421 (mt) cc_final: 0.7103 (mm) REVERT: C 232 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6977 (m-70) REVERT: C 315 GLN cc_start: 0.8642 (mm110) cc_final: 0.8353 (mm-40) REVERT: C 317 PHE cc_start: 0.7938 (t80) cc_final: 0.7677 (t80) REVERT: C 319 ASN cc_start: 0.8599 (m110) cc_final: 0.8218 (t0) REVERT: C 335 MET cc_start: 0.7988 (mmm) cc_final: 0.7697 (mmp) REVERT: C 390 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8022 (ttp-170) REVERT: C 479 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8453 (mmt-90) REVERT: D 38 MET cc_start: 0.8288 (tmm) cc_final: 0.8004 (tmm) REVERT: D 45 PHE cc_start: 0.7904 (t80) cc_final: 0.7404 (t80) REVERT: D 47 MET cc_start: 0.7681 (tpt) cc_final: 0.7105 (tpp) REVERT: D 119 GLN cc_start: 0.8228 (pt0) cc_final: 0.7995 (pt0) REVERT: D 177 ILE cc_start: 0.7293 (mt) cc_final: 0.7076 (mm) REVERT: D 232 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6931 (m-70) REVERT: D 317 PHE cc_start: 0.7846 (t80) cc_final: 0.7520 (t80) REVERT: D 319 ASN cc_start: 0.8651 (m110) cc_final: 0.8290 (t0) REVERT: D 390 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8081 (ttp-110) REVERT: D 476 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9044 (tt) outliers start: 101 outliers final: 79 residues processed: 355 average time/residue: 0.2484 time to fit residues: 133.0805 Evaluate side-chains 358 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 263 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 494 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN C 125 GLN C 281 ASN D 125 GLN D 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16148 Z= 0.186 Angle : 0.544 9.959 21832 Z= 0.282 Chirality : 0.039 0.205 2492 Planarity : 0.003 0.043 2676 Dihedral : 5.266 42.607 2236 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.63 % Allowed : 23.97 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1880 helix: 2.04 (0.15), residues: 1120 sheet: -0.74 (0.29), residues: 276 loop : -1.56 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 272 HIS 0.002 0.001 HIS C 252 PHE 0.017 0.001 PHE A 497 TYR 0.015 0.001 TYR A 481 ARG 0.006 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 275 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.5942 (p90) REVERT: A 47 MET cc_start: 0.7772 (tpt) cc_final: 0.7202 (tpp) REVERT: A 232 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.7007 (m-70) REVERT: A 283 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7813 (p90) REVERT: A 319 ASN cc_start: 0.8634 (m110) cc_final: 0.8413 (p0) REVERT: A 344 MET cc_start: 0.8432 (ttm) cc_final: 0.8089 (ttp) REVERT: A 467 MET cc_start: 0.9155 (mmm) cc_final: 0.8849 (mmm) REVERT: B 38 MET cc_start: 0.7992 (tmm) cc_final: 0.7706 (ppp) REVERT: B 44 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6057 (p90) REVERT: B 47 MET cc_start: 0.7522 (tpp) cc_final: 0.7258 (tpp) REVERT: B 56 ARG cc_start: 0.7674 (ttt-90) cc_final: 0.7261 (tmm160) REVERT: B 232 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.7051 (m-70) REVERT: B 271 ASP cc_start: 0.7323 (t0) cc_final: 0.7073 (t0) REVERT: B 283 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.7857 (p90) REVERT: B 286 MET cc_start: 0.8813 (mmm) cc_final: 0.8533 (tpp) REVERT: B 319 ASN cc_start: 0.8650 (m110) cc_final: 0.8235 (t0) REVERT: B 335 MET cc_start: 0.7666 (mmm) cc_final: 0.7323 (mmp) REVERT: B 363 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 418 CYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8543 (m) REVERT: B 476 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8948 (tt) REVERT: B 479 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8407 (mmt-90) REVERT: C 44 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6005 (p90) REVERT: C 47 MET cc_start: 0.7895 (tpt) cc_final: 0.7414 (tpp) REVERT: C 72 MET cc_start: 0.8783 (mmp) cc_final: 0.8570 (mmm) REVERT: C 177 ILE cc_start: 0.7414 (mt) cc_final: 0.7100 (mm) REVERT: C 232 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6913 (m-70) REVERT: C 319 ASN cc_start: 0.8548 (m110) cc_final: 0.8182 (t0) REVERT: C 335 MET cc_start: 0.7699 (mmm) cc_final: 0.7318 (mmp) REVERT: C 390 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8004 (ttp-170) REVERT: C 479 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8415 (mmt-90) REVERT: D 38 MET cc_start: 0.8305 (tmm) cc_final: 0.8016 (tmm) REVERT: D 45 PHE cc_start: 0.7914 (t80) cc_final: 0.7440 (t80) REVERT: D 47 MET cc_start: 0.7640 (tpt) cc_final: 0.7066 (tpp) REVERT: D 119 GLN cc_start: 0.8157 (pt0) cc_final: 0.7933 (pt0) REVERT: D 177 ILE cc_start: 0.7296 (mt) cc_final: 0.7091 (mm) REVERT: D 232 HIS cc_start: 0.7232 (OUTLIER) cc_final: 0.6856 (m-70) REVERT: D 317 PHE cc_start: 0.7878 (t80) cc_final: 0.7623 (t80) REVERT: D 319 ASN cc_start: 0.8640 (m110) cc_final: 0.8296 (t0) REVERT: D 390 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7925 (ttp-170) REVERT: D 476 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9034 (tt) outliers start: 98 outliers final: 74 residues processed: 353 average time/residue: 0.2618 time to fit residues: 139.8593 Evaluate side-chains 352 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 262 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.0050 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN B 456 ASN C 125 GLN C 281 ASN D 125 GLN D 281 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16148 Z= 0.188 Angle : 0.543 9.805 21832 Z= 0.281 Chirality : 0.039 0.208 2492 Planarity : 0.003 0.043 2676 Dihedral : 5.208 42.805 2236 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.75 % Allowed : 23.68 % Favored : 70.57 % 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: 1.19 (0.19), residues: 1880 helix: 2.16 (0.15), residues: 1112 sheet: -0.62 (0.30), residues: 276 loop : -1.59 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 272 HIS 0.002 0.001 HIS C 252 PHE 0.017 0.002 PHE A 317 TYR 0.015 0.001 TYR A 481 ARG 0.005 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 272 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.5942 (p90) REVERT: A 45 PHE cc_start: 0.8219 (t80) cc_final: 0.7955 (t80) REVERT: A 47 MET cc_start: 0.7782 (tpt) cc_final: 0.7223 (tpp) REVERT: A 232 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.7027 (m-70) REVERT: A 283 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.7802 (p90) REVERT: A 319 ASN cc_start: 0.8562 (m110) cc_final: 0.8285 (t0) REVERT: A 344 MET cc_start: 0.8400 (ttm) cc_final: 0.8061 (ttp) REVERT: A 467 MET cc_start: 0.9156 (mmm) cc_final: 0.8844 (mmm) REVERT: B 44 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6008 (p90) REVERT: B 47 MET cc_start: 0.7528 (tpp) cc_final: 0.7263 (tpp) REVERT: B 56 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.7268 (tmm160) REVERT: B 232 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.7035 (m-70) REVERT: B 271 ASP cc_start: 0.7322 (t0) cc_final: 0.7022 (t0) REVERT: B 283 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7856 (p90) REVERT: B 286 MET cc_start: 0.8826 (mmm) cc_final: 0.8548 (tpp) REVERT: B 335 MET cc_start: 0.7662 (mmm) cc_final: 0.7334 (mmp) REVERT: B 363 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 418 CYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8517 (m) REVERT: B 479 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8409 (mmt-90) REVERT: C 44 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6011 (p90) REVERT: C 47 MET cc_start: 0.7880 (tpt) cc_final: 0.7402 (tpp) REVERT: C 72 MET cc_start: 0.8771 (mmp) cc_final: 0.8569 (mmm) REVERT: C 156 MET cc_start: 0.8300 (tpp) cc_final: 0.8076 (ttt) REVERT: C 177 ILE cc_start: 0.7432 (mt) cc_final: 0.7111 (mm) REVERT: C 232 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6899 (m-70) REVERT: C 335 MET cc_start: 0.7753 (mmm) cc_final: 0.7357 (mmp) REVERT: C 390 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7999 (ttp-170) REVERT: C 432 ILE cc_start: 0.8714 (tp) cc_final: 0.8485 (tp) REVERT: C 479 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8400 (mmt-90) REVERT: D 38 MET cc_start: 0.8299 (tmm) cc_final: 0.8006 (tmm) REVERT: D 47 MET cc_start: 0.7648 (tpt) cc_final: 0.7067 (tpp) REVERT: D 119 GLN cc_start: 0.8152 (pt0) cc_final: 0.7940 (pt0) REVERT: D 232 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6851 (m-70) REVERT: D 317 PHE cc_start: 0.7901 (t80) cc_final: 0.7666 (t80) REVERT: D 319 ASN cc_start: 0.8575 (m110) cc_final: 0.8238 (t0) REVERT: D 390 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7908 (ttp-170) REVERT: D 476 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9023 (tt) outliers start: 100 outliers final: 75 residues processed: 350 average time/residue: 0.2456 time to fit residues: 130.3530 Evaluate side-chains 346 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 256 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 456 ASN C 125 GLN C 281 ASN D 125 GLN D 281 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16148 Z= 0.173 Angle : 0.544 9.768 21832 Z= 0.280 Chirality : 0.039 0.212 2492 Planarity : 0.003 0.044 2676 Dihedral : 5.120 42.895 2236 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 5.11 % Allowed : 24.77 % Favored : 70.11 % 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: 1.29 (0.19), residues: 1880 helix: 2.23 (0.15), residues: 1112 sheet: -0.52 (0.30), residues: 276 loop : -1.58 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 475 HIS 0.003 0.001 HIS C 252 PHE 0.017 0.001 PHE A 317 TYR 0.015 0.001 TYR A 481 ARG 0.005 0.000 ARG B 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 267 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.5937 (p90) REVERT: A 45 PHE cc_start: 0.8175 (t80) cc_final: 0.7943 (t80) REVERT: A 47 MET cc_start: 0.7746 (tpt) cc_final: 0.7198 (tpp) REVERT: A 232 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6988 (m90) REVERT: A 283 HIS cc_start: 0.8525 (OUTLIER) cc_final: 0.7861 (p90) REVERT: A 344 MET cc_start: 0.8437 (ttm) cc_final: 0.8133 (ttp) REVERT: A 460 MET cc_start: 0.9089 (ttm) cc_final: 0.8797 (mtt) REVERT: A 467 MET cc_start: 0.9137 (mmm) cc_final: 0.8843 (mmm) REVERT: B 38 MET cc_start: 0.7766 (tmm) cc_final: 0.7533 (ppp) REVERT: B 44 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6057 (p90) REVERT: B 47 MET cc_start: 0.7608 (tpp) cc_final: 0.7359 (tpp) REVERT: B 56 ARG cc_start: 0.7813 (ttt-90) cc_final: 0.7264 (tmm160) REVERT: B 232 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.7035 (m-70) REVERT: B 271 ASP cc_start: 0.7350 (t0) cc_final: 0.7101 (t0) REVERT: B 283 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7840 (p90) REVERT: B 286 MET cc_start: 0.8886 (mmm) cc_final: 0.8643 (tpp) REVERT: B 335 MET cc_start: 0.7613 (mmm) cc_final: 0.7262 (mmp) REVERT: B 363 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 418 CYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8484 (m) REVERT: B 479 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8367 (mmt-90) REVERT: C 44 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6016 (p90) REVERT: C 47 MET cc_start: 0.7878 (tpt) cc_final: 0.7395 (tpp) REVERT: C 156 MET cc_start: 0.8315 (tpp) cc_final: 0.8099 (ttt) REVERT: C 177 ILE cc_start: 0.7538 (mt) cc_final: 0.7252 (mm) REVERT: C 232 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.6878 (m-70) REVERT: C 335 MET cc_start: 0.7724 (mmm) cc_final: 0.7348 (mmp) REVERT: C 390 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8032 (ttp-110) REVERT: C 432 ILE cc_start: 0.8695 (tp) cc_final: 0.8458 (tp) REVERT: C 460 MET cc_start: 0.9280 (ttm) cc_final: 0.8579 (ttm) REVERT: C 479 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8386 (mmt-90) REVERT: D 38 MET cc_start: 0.8357 (tmm) cc_final: 0.8023 (tmm) REVERT: D 47 MET cc_start: 0.7649 (tpt) cc_final: 0.7059 (tpp) REVERT: D 232 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6903 (m-70) REVERT: D 317 PHE cc_start: 0.7883 (t80) cc_final: 0.7648 (t80) REVERT: D 319 ASN cc_start: 0.8679 (m110) cc_final: 0.8377 (t0) REVERT: D 390 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7810 (ttp80) REVERT: D 460 MET cc_start: 0.9090 (ttm) cc_final: 0.8781 (mtt) REVERT: D 476 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9001 (tt) outliers start: 89 outliers final: 65 residues processed: 337 average time/residue: 0.2563 time to fit residues: 130.8825 Evaluate side-chains 342 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 262 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.0470 chunk 131 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN C 125 GLN C 281 ASN D 125 GLN D 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125844 restraints weight = 22486.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125299 restraints weight = 16784.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126806 restraints weight = 18281.729| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16148 Z= 0.148 Angle : 0.540 9.660 21832 Z= 0.275 Chirality : 0.039 0.191 2492 Planarity : 0.003 0.044 2676 Dihedral : 5.056 42.170 2236 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.43 % Allowed : 25.46 % Favored : 70.11 % 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: 1.41 (0.19), residues: 1880 helix: 2.33 (0.15), residues: 1112 sheet: -0.45 (0.31), residues: 276 loop : -1.57 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 475 HIS 0.003 0.001 HIS C 252 PHE 0.017 0.001 PHE A 317 TYR 0.014 0.001 TYR A 481 ARG 0.005 0.000 ARG B 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.03 seconds wall clock time: 60 minutes 16.81 seconds (3616.81 seconds total)