Starting phenix.real_space_refine on Thu Feb 22 02:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds3_27682/02_2024/8ds3_27682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds3_27682/02_2024/8ds3_27682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds3_27682/02_2024/8ds3_27682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds3_27682/02_2024/8ds3_27682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds3_27682/02_2024/8ds3_27682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds3_27682/02_2024/8ds3_27682_updated.pdb" } resolution = 3.07 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= 0.021 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 154 5.16 5 C 21312 2.51 5 N 5357 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "B GLU 775": "OE1" <-> "OE2" Residue "B GLU 797": "OE1" <-> "OE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C GLU 618": "OE1" <-> "OE2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C GLU 788": "OE1" <-> "OE2" Residue "C GLU 797": "OE1" <-> "OE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 354": "OE1" <-> "OE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 473": "OE1" <-> "OE2" Residue "E TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 519": "OE1" <-> "OE2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E ASP 538": "OD1" <-> "OD2" Residue "E ASP 620": "OD1" <-> "OD2" Residue "E GLU 760": "OE1" <-> "OE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 378": "OD1" <-> "OD2" Residue "F ASP 381": "OD1" <-> "OD2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 593": "OE1" <-> "OE2" Residue "F GLU 602": "OE1" <-> "OE2" Residue "F PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F GLU 724": "OE1" <-> "OE2" Residue "F GLU 770": "OE1" <-> "OE2" Residue "F GLU 798": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32601 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "C" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5751 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 16.91, per 1000 atoms: 0.52 Number of scatterers: 32601 At special positions: 0 Unit cell: (140.432, 137.288, 194.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 9 15.00 O 5769 8.00 N 5357 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.02 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 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 Time building additional restraints: 13.08 Conformation dependent library (CDL) restraints added in 5.5 seconds 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7542 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 165 helices and 20 sheets defined 45.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 120 through 140 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 147 through 164 removed outlier: 3.668A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 234 through 254 Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.840A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 313 through 344 removed outlier: 4.383A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 321 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 322 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 329 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 335 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.527A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.783A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.654A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 4.238A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.076A pdb=" N VAL A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 634 through 637 removed outlier: 3.692A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 680 through 683 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 788 through 792 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 140 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 147 through 164 removed outlier: 3.789A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 259 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.906A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 371 through 382 Processing helix chain 'B' and resid 384 through 393 removed outlier: 3.817A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.740A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 511 through 514 No H-bonds generated for 'chain 'B' and resid 511 through 514' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.911A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 542 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 removed outlier: 4.517A pdb=" N VAL B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 680 through 683 removed outlier: 3.508A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 680 through 683' Processing helix chain 'B' and resid 702 through 706 Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 748 through 751 No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 771 through 773 No H-bonds generated for 'chain 'B' and resid 771 through 773' Processing helix chain 'B' and resid 788 through 791 No H-bonds generated for 'chain 'B' and resid 788 through 791' Processing helix chain 'B' and resid 796 through 807 Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 23 through 48 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 140 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.690A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 234 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.748A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 343 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.514A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 393 removed outlier: 3.920A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 410 Processing helix chain 'C' and resid 413 through 418 removed outlier: 4.003A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 485 through 493 Processing helix chain 'C' and resid 537 through 540 Processing helix chain 'C' and resid 560 through 567 removed outlier: 4.276A pdb=" N VAL C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 611 No H-bonds generated for 'chain 'C' and resid 608 through 611' Processing helix chain 'C' and resid 630 through 637 removed outlier: 4.063A pdb=" N ILE C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 660 Processing helix chain 'C' and resid 679 through 683 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 726 through 729 Processing helix chain 'C' and resid 748 through 752 Processing helix chain 'C' and resid 771 through 774 Processing helix chain 'C' and resid 788 through 793 removed outlier: 4.948A pdb=" N THR C 793 " --> pdb=" O ASP C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 807 Processing helix chain 'D' and resid 17 through 20 Processing helix chain 'D' and resid 23 through 48 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 120 through 145 Proline residue: D 126 - end of helix removed outlier: 5.005A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.905A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 254 Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.670A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 370 through 382 Processing helix chain 'D' and resid 384 through 393 removed outlier: 4.009A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 Processing helix chain 'E' and resid 23 through 48 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 140 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 147 through 164 removed outlier: 3.766A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 234 through 254 Processing helix chain 'E' and resid 259 through 288 removed outlier: 4.800A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 342 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 371 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.871A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 413 through 419 Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 463 through 467 Processing helix chain 'E' and resid 485 through 493 Processing helix chain 'E' and resid 511 through 513 No H-bonds generated for 'chain 'E' and resid 511 through 513' Processing helix chain 'E' and resid 538 through 540 No H-bonds generated for 'chain 'E' and resid 538 through 540' Processing helix chain 'E' and resid 560 through 567 removed outlier: 4.415A pdb=" N VAL E 567 " --> pdb=" O THR E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 612 No H-bonds generated for 'chain 'E' and resid 610 through 612' Processing helix chain 'E' and resid 633 through 637 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 633 through 637' Processing helix chain 'E' and resid 656 through 660 Processing helix chain 'E' and resid 680 through 683 Processing helix chain 'E' and resid 702 through 706 Processing helix chain 'E' and resid 725 through 729 Processing helix chain 'E' and resid 748 through 752 Processing helix chain 'E' and resid 771 through 775 Processing helix chain 'E' and resid 789 through 792 No H-bonds generated for 'chain 'E' and resid 789 through 792' Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 23 through 46 Processing helix chain 'F' and resid 105 through 118 Processing helix chain 'F' and resid 122 through 142 Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 149 through 167 removed outlier: 3.882A pdb=" N SER F 153 " --> pdb=" O PRO F 149 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 257 through 286 removed outlier: 4.882A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 342 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 368 through 380 Processing helix chain 'F' and resid 382 through 392 removed outlier: 3.718A pdb=" N LYS F 386 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 Processing helix chain 'F' and resid 411 through 417 Processing helix chain 'F' and resid 438 through 442 Processing helix chain 'F' and resid 461 through 465 Processing helix chain 'F' and resid 483 through 491 Processing helix chain 'F' and resid 510 through 512 No H-bonds generated for 'chain 'F' and resid 510 through 512' Processing helix chain 'F' and resid 535 through 537 No H-bonds generated for 'chain 'F' and resid 535 through 537' Processing helix chain 'F' and resid 558 through 565 removed outlier: 5.277A pdb=" N SER F 565 " --> pdb=" O VAL F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 586 No H-bonds generated for 'chain 'F' and resid 583 through 586' Processing helix chain 'F' and resid 606 through 610 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.892A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 658 Processing helix chain 'F' and resid 700 through 704 Processing helix chain 'F' and resid 724 through 727 No H-bonds generated for 'chain 'F' and resid 724 through 727' Processing helix chain 'F' and resid 746 through 748 No H-bonds generated for 'chain 'F' and resid 746 through 748' Processing helix chain 'F' and resid 769 through 771 No H-bonds generated for 'chain 'F' and resid 769 through 771' Processing helix chain 'F' and resid 786 through 789 No H-bonds generated for 'chain 'F' and resid 786 through 789' Processing helix chain 'F' and resid 794 through 801 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= B, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.974A pdb=" N VAL A 450 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU A 432 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS A 452 " --> pdb=" O LEU A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 497 through 501 removed outlier: 6.183A pdb=" N GLU A 520 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE A 500 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A 522 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 548 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU A 523 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG A 550 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 571 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 551 " --> pdb=" O LYS A 571 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER A 573 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU A 595 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE A 574 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU A 597 " --> pdb=" O ILE A 574 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 618 through 620 removed outlier: 6.848A pdb=" N CYS A 643 " --> pdb=" O ILE A 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 666 through 668 removed outlier: 6.434A pdb=" N TYR A 689 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN A 712 " --> pdb=" O LEU A 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 735 through 737 removed outlier: 7.239A pdb=" N GLN A 758 " --> pdb=" O LEU A 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= H, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.415A pdb=" N VAL B 450 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 432 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS B 452 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU B 473 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU B 453 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TRP B 475 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA B 497 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU B 476 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS B 499 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU B 520 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE B 500 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS B 522 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.634A pdb=" N LYS B 571 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 551 " --> pdb=" O LYS B 571 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER B 573 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU B 595 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE B 574 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU B 597 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 618 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 598 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP B 620 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS B 643 " --> pdb=" O ILE B 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 666 through 668 removed outlier: 6.554A pdb=" N TYR B 689 " --> pdb=" O LEU B 667 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= L, first strand: chain 'C' and resid 429 through 433 removed outlier: 7.776A pdb=" N VAL C 450 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU C 432 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS C 452 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU C 473 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU C 453 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP C 475 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA C 497 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 476 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS C 499 " --> pdb=" O LEU C 476 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 459 through 461 Processing sheet with id= N, first strand: chain 'C' and resid 520 through 524 removed outlier: 5.737A pdb=" N VAL C 548 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU C 523 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG C 550 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS C 571 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 551 " --> pdb=" O LYS C 571 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER C 573 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLU C 595 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE C 574 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU C 597 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU C 618 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 598 " --> pdb=" O GLU C 618 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP C 620 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N CYS C 643 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG C 666 " --> pdb=" O LEU C 644 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= P, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.556A pdb=" N LEU E 55 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 429 through 433 removed outlier: 7.754A pdb=" N VAL E 450 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU E 432 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS E 452 " --> pdb=" O LEU E 432 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU E 473 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU E 453 " --> pdb=" O GLU E 473 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TRP E 475 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA E 497 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU E 476 " --> pdb=" O ALA E 497 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS E 499 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU E 520 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE E 500 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS E 522 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL E 548 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU E 523 " --> pdb=" O VAL E 548 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG E 550 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS E 571 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU E 551 " --> pdb=" O LYS E 571 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 573 " --> pdb=" O LEU E 551 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU E 595 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE E 574 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLU E 597 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU E 618 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU E 598 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP E 620 " --> pdb=" O LEU E 598 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN E 712 " --> pdb=" O LEU E 690 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA E 735 " --> pdb=" O LEU E 713 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN E 758 " --> pdb=" O LEU E 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'F' and resid 52 through 56 Processing sheet with id= T, first strand: chain 'F' and resid 418 through 420 removed outlier: 7.755A pdb=" N SER F 448 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LEU F 430 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS F 450 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU F 471 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU F 451 " --> pdb=" O GLU F 471 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS F 473 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 495 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU F 474 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER F 497 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU F 518 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL F 498 " --> pdb=" O GLU F 518 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR F 520 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE F 500 " --> pdb=" O TYR F 520 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL F 522 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE F 546 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU F 521 " --> pdb=" O ILE F 546 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER F 548 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY F 523 " --> pdb=" O SER F 548 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS F 569 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE F 549 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS F 571 " --> pdb=" O ILE F 549 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU F 593 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL F 572 " --> pdb=" O GLU F 593 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU F 595 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU F 616 " --> pdb=" O LEU F 594 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU F 596 " --> pdb=" O GLU F 616 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP F 618 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL F 641 " --> pdb=" O LEU F 617 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU F 619 " --> pdb=" O VAL F 641 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS F 643 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG F 664 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR F 687 " --> pdb=" O LEU F 665 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR F 710 " --> pdb=" O LEU F 688 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR F 733 " --> pdb=" O PHE F 711 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3120 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: 10.54 Time building geometry restraints manager: 14.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6102 1.33 - 1.45: 7878 1.45 - 1.57: 19088 1.57 - 1.70: 14 1.70 - 1.82: 225 Bond restraints: 33307 Sorted by residual: bond pdb=" C10 PEE A 902 " pdb=" O4 PEE A 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE D 902 " pdb=" O4 PEE D 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C10 PEE E 903 " pdb=" O4 PEE E 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 33302 not shown) Histogram of bond angle deviations from ideal: 90.55 - 99.34: 13 99.34 - 108.14: 1423 108.14 - 116.94: 22120 116.94 - 125.74: 20869 125.74 - 134.54: 552 Bond angle restraints: 44977 Sorted by residual: angle pdb=" O1P PEE F 904 " pdb=" P PEE F 904 " pdb=" O2P PEE F 904 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.26 -13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.20 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.18 -13.75 3.00e+00 1.11e-01 2.10e+01 ... (remaining 44972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 19657 35.96 - 71.93: 559 71.93 - 107.89: 33 107.89 - 143.85: 14 143.85 - 179.82: 16 Dihedral angle restraints: 20279 sinusoidal: 8697 harmonic: 11582 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 50.48 42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA LYS B 589 " pdb=" C LYS B 589 " pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU E 468 " pdb=" C LEU E 468 " pdb=" N THR E 469 " pdb=" CA THR E 469 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 20276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4898 0.098 - 0.195: 195 0.195 - 0.293: 3 0.293 - 0.390: 3 0.390 - 0.488: 8 Chirality restraints: 5107 Sorted by residual: chirality pdb=" CB ILE A 629 " pdb=" CA ILE A 629 " pdb=" CG1 ILE A 629 " pdb=" CG2 ILE A 629 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C2 PEE B 904 " pdb=" C1 PEE B 904 " pdb=" C3 PEE B 904 " pdb=" O2 PEE B 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 5104 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.032 2.00e-02 2.50e+03 2.93e-02 2.15e+01 pdb=" CG TRP A 475 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 462 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 463 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 724 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 725 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 725 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 725 " -0.046 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3303 2.75 - 3.29: 32902 3.29 - 3.82: 56630 3.82 - 4.36: 69198 4.36 - 4.90: 113304 Nonbonded interactions: 275337 Sorted by model distance: nonbonded pdb=" O SER E 395 " pdb=" OG SER E 398 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" O MET F 300 " model vdw 2.213 2.440 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.232 2.440 nonbonded pdb=" O SER D 166 " pdb=" OG1 THR D 169 " model vdw 2.233 2.440 nonbonded pdb=" O SER B 166 " pdb=" OG1 THR B 169 " model vdw 2.233 2.440 ... (remaining 275332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 808 or resid 901 or (resid 902 through 903 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 808 or resid 901 through 903)) selection = (chain 'C' and (resid 15 through 808 or resid 901 or (resid 902 through 903 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 808 or resid 901 or (resid 902 through 903 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 16.760 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 83.940 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.180 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 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 : 0.005 0.152 33307 Z= 0.376 Angle : 0.898 13.848 44977 Z= 0.459 Chirality : 0.048 0.488 5107 Planarity : 0.006 0.093 5516 Dihedral : 17.578 179.817 12686 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.28 % Allowed : 18.38 % Favored : 81.34 % 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: -1.35 (0.13), residues: 3852 helix: -0.29 (0.12), residues: 1852 sheet: -1.57 (0.29), residues: 358 loop : -1.33 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP A 475 HIS 0.011 0.001 HIS E 694 PHE 0.041 0.002 PHE F 488 TYR 0.053 0.002 TYR F 687 ARG 0.009 0.001 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 333 time to evaluate : 4.969 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: symmetry clash revert: symmetry clash REVERT: C 438 ILE cc_start: 0.7420 (pt) cc_final: 0.7125 (pt) REVERT: F 145 TRP cc_start: 0.5443 (t60) cc_final: 0.5105 (t60) outliers start: 10 outliers final: 5 residues processed: 339 average time/residue: 0.4462 time to fit residues: 248.2279 Evaluate side-chains 297 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 324 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 301 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 349 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS C 377 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 409 ASN ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 694 HIS F 60 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN F 424 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33307 Z= 0.300 Angle : 0.573 12.285 44977 Z= 0.290 Chirality : 0.042 0.284 5107 Planarity : 0.004 0.066 5516 Dihedral : 14.211 179.274 4689 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 17.77 % Favored : 80.23 % 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: -0.84 (0.14), residues: 3852 helix: 0.25 (0.12), residues: 1862 sheet: -1.48 (0.29), residues: 366 loop : -1.19 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 475 HIS 0.007 0.001 HIS A 694 PHE 0.023 0.002 PHE D 324 TYR 0.024 0.002 TYR C 281 ARG 0.006 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 302 time to evaluate : 4.613 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 410 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6483 (pp20) REVERT: C 37 MET cc_start: 0.7834 (mmm) cc_final: 0.7616 (mmp) REVERT: D 309 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7258 (ttm-80) REVERT: E 104 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7948 (t70) REVERT: E 443 PHE cc_start: 0.7539 (m-80) cc_final: 0.7275 (m-80) REVERT: E 479 THR cc_start: 0.8039 (m) cc_final: 0.7652 (p) outliers start: 72 outliers final: 33 residues processed: 356 average time/residue: 0.4672 time to fit residues: 272.6630 Evaluate side-chains 313 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 278 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 536 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 5.9990 chunk 108 optimal weight: 0.0570 chunk 290 optimal weight: 0.5980 chunk 238 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 350 optimal weight: 3.9990 chunk 378 optimal weight: 20.0000 chunk 311 optimal weight: 0.3980 chunk 347 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS A 695 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33307 Z= 0.229 Angle : 0.538 10.631 44977 Z= 0.273 Chirality : 0.040 0.221 5107 Planarity : 0.004 0.059 5516 Dihedral : 12.942 173.031 4681 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.30 % Allowed : 18.30 % Favored : 79.40 % 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: -0.66 (0.14), residues: 3852 helix: 0.43 (0.12), residues: 1855 sheet: -1.30 (0.30), residues: 364 loop : -1.17 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 475 HIS 0.010 0.001 HIS E 104 PHE 0.029 0.001 PHE D 324 TYR 0.032 0.001 TYR F 646 ARG 0.010 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 311 time to evaluate : 4.171 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 434 MET cc_start: 0.7183 (mpp) cc_final: 0.6396 (mpp) REVERT: A 438 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8700 (pt) REVERT: A 471 LEU cc_start: 0.7937 (tp) cc_final: 0.7711 (pp) REVERT: B 232 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5504 (tp) REVERT: C 37 MET cc_start: 0.7836 (mmm) cc_final: 0.7616 (mmp) REVERT: C 379 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7528 (mm) REVERT: C 769 LEU cc_start: 0.2916 (mt) cc_final: 0.2662 (mp) REVERT: D 309 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7283 (ttm-80) REVERT: E 244 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7844 (t80) REVERT: E 275 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8450 (t80) REVERT: E 394 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7054 (mt) REVERT: F 264 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6574 (ttm170) REVERT: F 503 MET cc_start: 0.6859 (mmt) cc_final: 0.6282 (tpp) REVERT: F 646 TYR cc_start: 0.6588 (m-80) cc_final: 0.6231 (m-80) outliers start: 83 outliers final: 48 residues processed: 371 average time/residue: 0.4331 time to fit residues: 261.4121 Evaluate side-chains 339 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 7.9990 chunk 263 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 167 optimal weight: 0.2980 chunk 235 optimal weight: 0.5980 chunk 351 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS A 695 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN C 408 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33307 Z= 0.171 Angle : 0.508 10.223 44977 Z= 0.255 Chirality : 0.039 0.183 5107 Planarity : 0.003 0.056 5516 Dihedral : 11.940 174.525 4681 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.88 % Allowed : 18.44 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3852 helix: 0.57 (0.12), residues: 1852 sheet: -1.22 (0.30), residues: 387 loop : -1.01 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 475 HIS 0.006 0.001 HIS E 104 PHE 0.025 0.001 PHE D 324 TYR 0.027 0.001 TYR F 646 ARG 0.003 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 300 time to evaluate : 3.253 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 438 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8703 (pt) REVERT: B 232 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5799 (tp) REVERT: C 356 ILE cc_start: 0.7636 (mm) cc_final: 0.7201 (mm) REVERT: C 769 LEU cc_start: 0.2795 (mt) cc_final: 0.2589 (mp) REVERT: D 168 TRP cc_start: 0.7498 (t-100) cc_final: 0.7206 (t-100) REVERT: D 309 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7224 (ttm-80) REVERT: E 275 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8266 (t80) REVERT: E 337 MET cc_start: 0.8165 (mmm) cc_final: 0.7849 (mtt) REVERT: E 394 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7138 (mt) REVERT: F 503 MET cc_start: 0.6913 (mmt) cc_final: 0.6312 (tpp) outliers start: 104 outliers final: 57 residues processed: 387 average time/residue: 0.4225 time to fit residues: 265.5511 Evaluate side-chains 348 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 287 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 153 optimal weight: 0.0370 chunk 317 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 334 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS A 695 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 566 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33307 Z= 0.184 Angle : 0.510 9.642 44977 Z= 0.256 Chirality : 0.039 0.168 5107 Planarity : 0.003 0.054 5516 Dihedral : 11.299 178.530 4679 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.57 % Allowed : 18.99 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3852 helix: 0.67 (0.13), residues: 1851 sheet: -1.14 (0.30), residues: 385 loop : -0.99 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 475 HIS 0.005 0.001 HIS C 522 PHE 0.032 0.001 PHE F 633 TYR 0.018 0.001 TYR C 683 ARG 0.010 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 307 time to evaluate : 3.812 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: symmetry clash revert: symmetry clash REVERT: A 438 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8728 (pt) REVERT: A 694 HIS cc_start: 0.7220 (m170) cc_final: 0.6873 (m170) REVERT: B 232 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5958 (tp) REVERT: B 298 ASP cc_start: 0.6430 (t0) cc_final: 0.6226 (t0) REVERT: C 379 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7526 (mm) REVERT: D 309 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7244 (ttm-80) REVERT: E 275 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8349 (t80) REVERT: E 394 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7243 (mt) REVERT: F 503 MET cc_start: 0.6822 (mmt) cc_final: 0.6258 (tpp) outliers start: 93 outliers final: 66 residues processed: 384 average time/residue: 0.4610 time to fit residues: 288.2467 Evaluate side-chains 354 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 283 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 10.0000 chunk 335 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 91 optimal weight: 0.0010 chunk 372 optimal weight: 0.4980 chunk 309 optimal weight: 0.0770 chunk 172 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33307 Z= 0.141 Angle : 0.505 11.600 44977 Z= 0.250 Chirality : 0.039 0.184 5107 Planarity : 0.003 0.052 5516 Dihedral : 10.639 178.537 4679 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.35 % Allowed : 19.44 % Favored : 78.21 % 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: -0.26 (0.14), residues: 3852 helix: 0.75 (0.13), residues: 1856 sheet: -1.16 (0.30), residues: 400 loop : -0.92 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 168 HIS 0.004 0.001 HIS E 499 PHE 0.019 0.001 PHE D 324 TYR 0.039 0.001 TYR F 646 ARG 0.004 0.000 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 301 time to evaluate : 4.125 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: symmetry clash revert: symmetry clash REVERT: A 694 HIS cc_start: 0.7196 (m170) cc_final: 0.6875 (m170) REVERT: A 697 LEU cc_start: 0.7353 (pp) cc_final: 0.6672 (mp) REVERT: B 46 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7162 (tp40) REVERT: B 232 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6031 (tp) REVERT: B 385 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6423 (mm) REVERT: C 379 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7670 (mm) REVERT: D 309 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.7234 (ttm-80) REVERT: E 275 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8058 (t80) REVERT: F 503 MET cc_start: 0.6637 (mmt) cc_final: 0.6200 (tpp) outliers start: 85 outliers final: 61 residues processed: 368 average time/residue: 0.4423 time to fit residues: 263.6117 Evaluate side-chains 343 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 277 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 660 ASN Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 371 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 171 optimal weight: 0.1980 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 758 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 66 ASN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33307 Z= 0.267 Angle : 0.540 10.586 44977 Z= 0.272 Chirality : 0.041 0.180 5107 Planarity : 0.003 0.052 5516 Dihedral : 10.555 176.900 4679 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.44 % Allowed : 19.21 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.32 (0.14), residues: 3852 helix: 0.66 (0.12), residues: 1861 sheet: -1.18 (0.29), residues: 408 loop : -0.91 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 168 HIS 0.005 0.001 HIS E 377 PHE 0.020 0.002 PHE B 353 TYR 0.037 0.002 TYR F 646 ARG 0.009 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 285 time to evaluate : 3.772 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: symmetry clash REVERT: A 265 MET cc_start: 0.7801 (tpp) cc_final: 0.7569 (tpp) REVERT: A 694 HIS cc_start: 0.7329 (m170) cc_final: 0.7087 (m170) REVERT: A 708 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6974 (tp-100) REVERT: B 46 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7203 (tp40) REVERT: B 232 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6184 (tp) REVERT: C 379 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7605 (mm) REVERT: C 769 LEU cc_start: 0.2988 (mt) cc_final: 0.2785 (mp) REVERT: D 309 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7163 (ttm-80) REVERT: E 394 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7219 (mt) REVERT: F 503 MET cc_start: 0.6703 (mmt) cc_final: 0.6080 (tpp) outliers start: 88 outliers final: 65 residues processed: 357 average time/residue: 0.4420 time to fit residues: 256.6251 Evaluate side-chains 347 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 277 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 590 ASN Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 252 optimal weight: 0.5980 chunk 183 optimal weight: 0.0170 chunk 34 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33307 Z= 0.191 Angle : 0.527 11.032 44977 Z= 0.262 Chirality : 0.040 0.205 5107 Planarity : 0.003 0.052 5516 Dihedral : 10.059 167.094 4679 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.35 % Allowed : 19.41 % Favored : 78.24 % 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: -0.24 (0.14), residues: 3852 helix: 0.74 (0.13), residues: 1852 sheet: -1.23 (0.29), residues: 414 loop : -0.85 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 511 HIS 0.004 0.001 HIS F 669 PHE 0.018 0.001 PHE D 324 TYR 0.030 0.001 TYR E 477 ARG 0.006 0.000 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 282 time to evaluate : 3.665 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: symmetry clash REVERT: A 694 HIS cc_start: 0.7354 (m170) cc_final: 0.7129 (m170) REVERT: B 46 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7170 (tp40) REVERT: B 232 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6294 (tp) REVERT: B 371 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.6674 (t70) REVERT: C 379 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7585 (mm) REVERT: C 769 LEU cc_start: 0.2975 (mt) cc_final: 0.2770 (mp) REVERT: D 309 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7235 (ttm-80) REVERT: E 394 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7234 (mt) REVERT: F 503 MET cc_start: 0.6618 (mmt) cc_final: 0.5970 (tpp) outliers start: 85 outliers final: 64 residues processed: 350 average time/residue: 0.4366 time to fit residues: 248.0325 Evaluate side-chains 338 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 269 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 452 LYS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 660 ASN Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 0.7980 chunk 355 optimal weight: 1.9990 chunk 324 optimal weight: 0.8980 chunk 345 optimal weight: 6.9990 chunk 208 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 312 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 chunk 344 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 HIS A 758 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33307 Z= 0.173 Angle : 0.523 13.109 44977 Z= 0.260 Chirality : 0.040 0.462 5107 Planarity : 0.003 0.053 5516 Dihedral : 9.490 157.427 4679 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.33 % Allowed : 19.60 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3852 helix: 0.79 (0.13), residues: 1843 sheet: -1.33 (0.28), residues: 429 loop : -0.77 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 475 HIS 0.004 0.001 HIS E 522 PHE 0.017 0.001 PHE E 250 TYR 0.026 0.001 TYR E 477 ARG 0.005 0.000 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 280 time to evaluate : 3.765 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.7484 (t70) cc_final: 0.7262 (t-90) REVERT: A 557 LYS cc_start: 0.8033 (pttp) cc_final: 0.7737 (tppt) REVERT: A 694 HIS cc_start: 0.7406 (m170) cc_final: 0.7179 (m170) REVERT: A 708 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6969 (tp-100) REVERT: A 738 LEU cc_start: 0.7616 (mp) cc_final: 0.7371 (mt) REVERT: B 46 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7161 (tp40) REVERT: B 371 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.6684 (t70) REVERT: C 379 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7574 (mm) REVERT: D 175 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5710 (tm-30) REVERT: D 309 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7227 (ttm-80) REVERT: F 503 MET cc_start: 0.6615 (mmt) cc_final: 0.5917 (tpp) outliers start: 84 outliers final: 69 residues processed: 351 average time/residue: 0.4552 time to fit residues: 262.1140 Evaluate side-chains 344 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 270 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 660 ASN Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 383 optimal weight: 10.0000 chunk 353 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN A 758 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33307 Z= 0.261 Angle : 0.554 12.483 44977 Z= 0.277 Chirality : 0.041 0.414 5107 Planarity : 0.004 0.109 5516 Dihedral : 9.351 152.892 4679 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.19 % Allowed : 19.71 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3852 helix: 0.70 (0.13), residues: 1853 sheet: -1.33 (0.28), residues: 429 loop : -0.81 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 509 HIS 0.005 0.001 HIS E 377 PHE 0.019 0.002 PHE A 324 TYR 0.028 0.001 TYR E 477 ARG 0.005 0.000 ARG C 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 274 time to evaluate : 3.842 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 431 HIS cc_start: 0.7492 (t70) cc_final: 0.7281 (t-90) REVERT: A 557 LYS cc_start: 0.7953 (pttp) cc_final: 0.7724 (pptt) REVERT: A 694 HIS cc_start: 0.7506 (m170) cc_final: 0.7268 (m170) REVERT: A 708 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7023 (tp-100) REVERT: B 46 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7172 (tp40) REVERT: B 371 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.6932 (t70) REVERT: C 379 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7621 (mm) REVERT: D 175 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5906 (tm-30) REVERT: D 309 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7169 (ttm-80) REVERT: D 383 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5968 (t70) REVERT: F 503 MET cc_start: 0.6576 (mmt) cc_final: 0.5887 (tpp) outliers start: 79 outliers final: 66 residues processed: 340 average time/residue: 0.4506 time to fit residues: 247.8701 Evaluate side-chains 337 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 265 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 590 ASN Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN A 758 GLN B 253 HIS B 404 GLN B 408 ASN B 478 HIS B 657 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.157157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108781 restraints weight = 68503.962| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.18 r_work: 0.3397 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 33307 Z= 0.453 Angle : 0.652 14.574 44977 Z= 0.331 Chirality : 0.045 0.430 5107 Planarity : 0.005 0.112 5516 Dihedral : 10.050 158.863 4679 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.13 % Allowed : 19.96 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.62 (0.14), residues: 3852 helix: 0.38 (0.12), residues: 1855 sheet: -1.28 (0.29), residues: 398 loop : -1.02 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP F 509 HIS 0.019 0.001 HIS E 694 PHE 0.029 0.003 PHE B 353 TYR 0.024 0.002 TYR E 477 ARG 0.006 0.001 ARG C 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7511.70 seconds wall clock time: 138 minutes 34.34 seconds (8314.34 seconds total)