Starting phenix.real_space_refine on Thu Feb 22 00:01:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f79_28898/02_2024/8f79_28898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f79_28898/02_2024/8f79_28898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f79_28898/02_2024/8f79_28898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f79_28898/02_2024/8f79_28898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f79_28898/02_2024/8f79_28898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f79_28898/02_2024/8f79_28898_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.060 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 6 5.49 5 S 154 5.16 5 C 21092 2.51 5 N 5349 2.21 5 O 5732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 67": "OD1" <-> "OD2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" 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 25": "OD1" <-> "OD2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 399": "OE1" <-> "OE2" 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 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "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 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D ASP 298": "OD1" <-> "OD2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 245": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 298": "OD1" <-> "OD2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 354": "OE1" <-> "OE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 177": "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 PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "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: 32333 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5916 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5912 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 27, 'TRANS': 688} Chain breaks: 2 Chain: "C" Number of atoms: 5898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5898 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Chain: "D" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2648 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 5905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5905 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 27, 'TRANS': 687} 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 64 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 93 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 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: 16.16, per 1000 atoms: 0.50 Number of scatterers: 32333 At special positions: 0 Unit cell: (145.672, 139.384, 192.832, 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 6 15.00 O 5732 8.00 N 5349 7.00 C 21092 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=2.04 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: 12.94 Conformation dependent library (CDL) restraints added in 5.9 seconds 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 161 helices and 20 sheets defined 45.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 4.188A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 103 through 116 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: 3.966A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.581A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 288 removed outlier: 3.920A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 345 removed outlier: 4.353A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 345 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.192A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.983A 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: 4.075A 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: 3.693A 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 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 23 through 48 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 145 Proline residue: B 126 - end of helix removed outlier: 4.569A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 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 288 removed outlier: 4.810A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 344 removed outlier: 3.544A pdb=" N CYS B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 384 through 393 removed outlier: 4.315A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.732A 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: 3.912A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.149A 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 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 23 through 49 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 145 Proline residue: C 126 - end of helix removed outlier: 4.619A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 234 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.842A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 344 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 384 through 394 removed outlier: 4.406A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (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: 4.275A 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: 3.745A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.732A 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 23 through 49 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: 4.602A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 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: 4.836A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 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 394 removed outlier: 4.537A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'E' and resid 23 through 49 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 145 Proline residue: E 126 - end of helix removed outlier: 4.498A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 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: 4.914A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 344 removed outlier: 3.577A pdb=" N SER E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.566A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.900A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.350A 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: 4.416A 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: 3.749A 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 23 through 48 removed outlier: 3.689A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) 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 144 through 147 No H-bonds generated for 'chain 'F' and resid 144 through 147' Processing helix chain 'F' and resid 149 through 167 Processing helix chain 'F' and resid 170 through 178 Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 257 through 283 Processing helix chain 'F' and resid 311 through 342 removed outlier: 4.588A pdb=" N HIS F 314 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU F 315 " --> pdb=" O MET F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 355 No H-bonds generated for 'chain 'F' and resid 352 through 355' Processing helix chain 'F' and resid 369 through 380 Processing helix chain 'F' and resid 382 through 391 removed outlier: 4.895A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 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: 5.276A 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 removed outlier: 3.601A pdb=" N VAL A 293 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 429 through 432 removed outlier: 6.952A pdb=" N VAL A 450 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU A 432 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 6.495A 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: 6.182A pdb=" N GLU A 520 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 7.032A 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: 6.324A 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: 7.079A pdb=" N ILE A 574 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 6.602A 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: 6.950A 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: 7.072A 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: 6.066A 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: 6.314A 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: 6.633A 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: 6.099A 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: 7.477A 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: 6.555A 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 52 through 56 Processing sheet with id= L, first strand: chain 'C' and resid 429 through 433 removed outlier: 7.777A pdb=" N VAL C 450 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 7.524A 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: 7.317A pdb=" N GLU C 473 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU C 453 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 6.474A 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: 6.367A 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: 6.197A 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: 8.391A 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: 7.482A 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: 3.636A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (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: 8.393A 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: 7.525A pdb=" N ILE E 500 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 5.993A 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: 7.294A pdb=" N LEU E 523 " --> pdb=" O VAL E 548 " (cutoff:3.500A) removed outlier: 6.272A 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: 6.727A pdb=" N SER E 573 " --> pdb=" O LEU E 551 " (cutoff:3.500A) removed outlier: 6.976A 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: 6.163A 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: 6.559A 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: 7.756A pdb=" N SER F 448 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 8.135A 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: 5.923A pdb=" N GLU F 518 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL F 498 " --> pdb=" O GLU F 518 " (cutoff:3.500A) removed outlier: 5.777A 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: 7.422A 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: 6.720A 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: 7.968A 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) 1143 hydrogen bonds defined for protein. 3105 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: 10.75 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9007 1.34 - 1.46: 5923 1.46 - 1.58: 17880 1.58 - 1.70: 11 1.70 - 1.82: 222 Bond restraints: 33043 Sorted by residual: bond pdb=" C10 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sigma weight residual 1.206 1.359 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.783 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" O4P PEE E 901 " pdb=" P PEE E 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" O4P PEE F 901 " pdb=" P PEE F 901 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 33038 not shown) Histogram of bond angle deviations from ideal: 90.60 - 99.36: 14 99.36 - 108.13: 1399 108.13 - 116.89: 21748 116.89 - 125.66: 20965 125.66 - 134.42: 552 Bond angle restraints: 44678 Sorted by residual: angle pdb=" N LEU A 344 " pdb=" CA LEU A 344 " pdb=" C LEU A 344 " ideal model delta sigma weight residual 111.69 118.08 -6.39 1.23e+00 6.61e-01 2.70e+01 angle pdb=" O1P PEE F 901 " pdb=" P PEE F 901 " pdb=" O2P PEE F 901 " ideal model delta sigma weight residual 119.43 133.32 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.23 -13.80 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.21 -13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 44673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 19437 35.76 - 71.52: 555 71.52 - 107.28: 39 107.28 - 143.04: 8 143.04 - 178.80: 9 Dihedral angle restraints: 20048 sinusoidal: 8478 harmonic: 11570 Sorted by residual: dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 295 " pdb=" CB CYS A 295 " ideal model delta sinusoidal sigma weight residual 93.00 36.75 56.25 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+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 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 20045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4843 0.098 - 0.195: 234 0.195 - 0.293: 8 0.293 - 0.391: 0 0.391 - 0.488: 3 Chirality restraints: 5088 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 5.96e+00 chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 5085 not shown) Planarity restraints: 5505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.032 2.00e-02 2.50e+03 2.92e-02 2.13e+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 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " -0.000 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 9.32e-02 1.39e+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 8.35e-02 1.12e+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 5502 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7458 2.79 - 3.32: 31116 3.32 - 3.85: 56172 3.85 - 4.37: 67608 4.37 - 4.90: 110261 Nonbonded interactions: 272615 Sorted by model distance: nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP F 689 " pdb=" OG SER F 691 " model vdw 2.264 2.440 nonbonded pdb=" O GLN C 560 " pdb=" OG1 THR C 563 " model vdw 2.266 2.440 nonbonded pdb=" O ARG B 492 " pdb=" OG1 THR B 517 " model vdw 2.272 2.440 nonbonded pdb=" O VAL E 591 " pdb=" ND2 ASN E 615 " model vdw 2.282 2.520 ... (remaining 272610 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 68 or resid 93 through 175 or resid 232 through \ 808 or resid 901 or (resid 902 and (name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 232 through \ 808 or (resid 901 and (name N or name C1 or name C10 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C2 or name C20 or name C4 or name C5 or name O1P or name O2 or name O2 \ P or name O3P or name O4 or name O4P or name P )) or (resid 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 808 or (resid 901 and (name N or name C1 or nam \ e C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C4 or name C5 o \ r name O1P or name O2 or name O2P or name O3P or name O4 or name O4P or name P ) \ ) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 175 or resid 232 through 808 or (resid 901 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3P or name O \ 4 or name O4P or name P )) or resid 902)) } 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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 18.940 Check model and map are aligned: 0.000 Set scattering table: 0.360 Process input model: 83.300 Find NCS groups from input model: 2.310 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 0.153 33043 Z= 0.323 Angle : 0.886 13.885 44678 Z= 0.487 Chirality : 0.047 0.488 5088 Planarity : 0.006 0.093 5505 Dihedral : 17.081 178.800 12461 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.39 % Allowed : 18.62 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3846 helix: -0.04 (0.12), residues: 1858 sheet: -1.47 (0.30), residues: 362 loop : -1.38 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP A 475 HIS 0.013 0.001 HIS C 155 PHE 0.044 0.002 PHE D 390 TYR 0.053 0.002 TYR F 687 ARG 0.012 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 543 time to evaluate : 3.879 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 434 MET cc_start: 0.8085 (mpp) cc_final: 0.7095 (mpp) REVERT: A 518 LEU cc_start: 0.7284 (tp) cc_final: 0.6861 (tp) REVERT: A 616 LEU cc_start: 0.5752 (mp) cc_final: 0.5480 (mt) REVERT: A 690 LEU cc_start: 0.8655 (tp) cc_final: 0.8155 (mp) REVERT: A 713 LEU cc_start: 0.8571 (tp) cc_final: 0.8320 (pt) REVERT: A 738 LEU cc_start: 0.8183 (mt) cc_final: 0.7811 (mt) REVERT: B 29 ASP cc_start: 0.7609 (m-30) cc_final: 0.7288 (m-30) REVERT: C 102 ASP cc_start: 0.8271 (m-30) cc_final: 0.7978 (m-30) REVERT: C 308 TYR cc_start: 0.9028 (m-80) cc_final: 0.8737 (m-80) REVERT: C 523 LEU cc_start: 0.4419 (mt) cc_final: 0.3979 (tt) REVERT: C 726 GLU cc_start: 0.6296 (tt0) cc_final: 0.6092 (tm-30) REVERT: D 142 PHE cc_start: 0.8329 (t80) cc_final: 0.8091 (t80) REVERT: D 385 LEU cc_start: 0.8196 (tp) cc_final: 0.7871 (tt) REVERT: F 510 MET cc_start: -0.0804 (mmp) cc_final: -0.1697 (mtm) REVERT: F 570 MET cc_start: -0.2196 (mmm) cc_final: -0.2462 (ttt) REVERT: F 800 MET cc_start: 0.0369 (tpt) cc_final: -0.2242 (ptm) outliers start: 14 outliers final: 3 residues processed: 555 average time/residue: 0.5231 time to fit residues: 439.2112 Evaluate side-chains 319 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 316 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 196 optimal weight: 30.0000 chunk 155 optimal weight: 0.3980 chunk 301 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 0.4980 chunk 224 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 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 49 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN B 478 HIS B 494 ASN B 617 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 650 HIS ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN E 418 GLN F 112 ASN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 ASN F 709 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33043 Z= 0.190 Angle : 0.590 12.792 44678 Z= 0.296 Chirality : 0.040 0.316 5088 Planarity : 0.004 0.104 5505 Dihedral : 10.857 177.870 4457 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.41 % Allowed : 19.23 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3846 helix: 0.50 (0.12), residues: 1866 sheet: -1.60 (0.29), residues: 384 loop : -1.14 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 475 HIS 0.006 0.001 HIS D 253 PHE 0.015 0.001 PHE A 433 TYR 0.026 0.001 TYR B 648 ARG 0.010 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 332 time to evaluate : 3.725 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: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8556 (m90) REVERT: A 235 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8251 (tptt) REVERT: A 518 LEU cc_start: 0.7239 (tp) cc_final: 0.6947 (tp) REVERT: A 616 LEU cc_start: 0.5768 (mp) cc_final: 0.5568 (mt) REVERT: B 616 LEU cc_start: 0.1998 (OUTLIER) cc_final: 0.1657 (mm) REVERT: C 102 ASP cc_start: 0.8382 (m-30) cc_final: 0.8116 (m-30) REVERT: C 523 LEU cc_start: 0.4552 (mt) cc_final: 0.4152 (tt) REVERT: D 142 PHE cc_start: 0.8331 (t80) cc_final: 0.8060 (t80) REVERT: D 154 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7740 (tt0) REVERT: D 250 PHE cc_start: 0.6461 (t80) cc_final: 0.6171 (t80) REVERT: D 375 MET cc_start: 0.7150 (tpp) cc_final: 0.6866 (mpp) REVERT: D 404 GLN cc_start: 0.7517 (tp-100) cc_final: 0.7227 (tp-100) REVERT: F 146 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.5488 (m-10) REVERT: F 510 MET cc_start: 0.0599 (mmp) cc_final: -0.1232 (mtm) REVERT: F 570 MET cc_start: -0.1996 (mmm) cc_final: -0.2420 (ttt) REVERT: F 800 MET cc_start: 0.0418 (tpt) cc_final: -0.2268 (ptm) outliers start: 87 outliers final: 41 residues processed: 397 average time/residue: 0.4963 time to fit residues: 314.5295 Evaluate side-chains 314 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 311 optimal weight: 0.6980 chunk 347 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS A 650 HIS ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN B 478 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN E 370 ASN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33043 Z= 0.229 Angle : 0.573 11.890 44678 Z= 0.285 Chirality : 0.040 0.252 5088 Planarity : 0.004 0.079 5505 Dihedral : 9.745 171.166 4455 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.41 % Allowed : 19.89 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3846 helix: 0.54 (0.12), residues: 1864 sheet: -1.69 (0.28), residues: 410 loop : -0.97 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 170 HIS 0.010 0.001 HIS C 253 PHE 0.014 0.001 PHE B 374 TYR 0.016 0.001 TYR F 259 ARG 0.011 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 293 time to evaluate : 3.525 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 104 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.8565 (m90) REVERT: A 235 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8205 (tptt) REVERT: A 239 GLN cc_start: 0.7700 (pt0) cc_final: 0.7216 (pt0) REVERT: A 243 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7981 (mp) REVERT: A 433 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 518 LEU cc_start: 0.7349 (tp) cc_final: 0.7076 (tp) REVERT: A 733 LEU cc_start: 0.7052 (mt) cc_final: 0.6718 (mt) REVERT: B 616 LEU cc_start: 0.2201 (OUTLIER) cc_final: 0.1795 (mm) REVERT: C 597 GLU cc_start: 0.4417 (mp0) cc_final: 0.2595 (mt-10) REVERT: D 145 LYS cc_start: 0.8409 (mmmt) cc_final: 0.6890 (pttt) REVERT: D 154 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7688 (tt0) REVERT: D 250 PHE cc_start: 0.6389 (t80) cc_final: 0.6032 (t80) REVERT: D 308 TYR cc_start: 0.9273 (m-80) cc_final: 0.9061 (m-80) REVERT: D 375 MET cc_start: 0.7287 (tpp) cc_final: 0.6892 (mpp) REVERT: D 404 GLN cc_start: 0.7571 (tp40) cc_final: 0.7317 (tp-100) REVERT: F 146 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: F 300 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: F 510 MET cc_start: 0.0286 (mmp) cc_final: -0.1352 (mtm) REVERT: F 800 MET cc_start: 0.0487 (tpt) cc_final: -0.2050 (ptt) outliers start: 87 outliers final: 50 residues processed: 359 average time/residue: 0.4298 time to fit residues: 251.0051 Evaluate side-chains 320 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 264 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 235 optimal weight: 0.4980 chunk 351 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 66 ASN A 522 HIS A 576 ASN A 657 GLN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 404 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 614 HIS E 709 ASN F 107 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33043 Z= 0.350 Angle : 0.600 9.775 44678 Z= 0.304 Chirality : 0.042 0.273 5088 Planarity : 0.004 0.043 5505 Dihedral : 9.070 153.062 4455 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.16 % Allowed : 19.78 % Favored : 77.06 % 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: -0.72 (0.14), residues: 3846 helix: 0.35 (0.12), residues: 1888 sheet: -1.72 (0.27), residues: 418 loop : -1.02 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 170 HIS 0.008 0.001 HIS E 312 PHE 0.018 0.002 PHE A 146 TYR 0.020 0.002 TYR D 281 ARG 0.008 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 281 time to evaluate : 4.126 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: A 104 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8638 (m90) REVERT: A 235 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8281 (tptt) REVERT: A 239 GLN cc_start: 0.7975 (pt0) cc_final: 0.7595 (pt0) REVERT: A 243 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 433 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7049 (t80) REVERT: A 488 LEU cc_start: 0.4266 (OUTLIER) cc_final: 0.4020 (mt) REVERT: A 518 LEU cc_start: 0.7441 (tp) cc_final: 0.7135 (tp) REVERT: A 733 LEU cc_start: 0.6957 (mt) cc_final: 0.6565 (mt) REVERT: B 616 LEU cc_start: 0.2345 (OUTLIER) cc_final: 0.1861 (mm) REVERT: D 145 LYS cc_start: 0.8555 (mmmt) cc_final: 0.7134 (pttt) REVERT: D 154 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7652 (tt0) REVERT: D 404 GLN cc_start: 0.7464 (tp40) cc_final: 0.7174 (tp-100) REVERT: F 146 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.5795 (m-10) REVERT: F 300 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7127 (mtp) outliers start: 114 outliers final: 64 residues processed: 376 average time/residue: 0.4170 time to fit residues: 258.2198 Evaluate side-chains 320 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 249 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 277 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 317 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 334 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 576 ASN A 708 GLN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33043 Z= 0.266 Angle : 0.557 10.901 44678 Z= 0.279 Chirality : 0.040 0.219 5088 Planarity : 0.004 0.040 5505 Dihedral : 8.202 153.004 4455 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.72 % Allowed : 21.17 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3846 helix: 0.42 (0.12), residues: 1877 sheet: -1.67 (0.27), residues: 417 loop : -0.92 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 170 HIS 0.006 0.001 HIS F 598 PHE 0.016 0.001 PHE B 443 TYR 0.017 0.002 TYR F 259 ARG 0.007 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 260 time to evaluate : 3.785 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 104 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.8579 (m90) REVERT: A 239 GLN cc_start: 0.7957 (pt0) cc_final: 0.7627 (pt0) REVERT: A 243 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 433 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 434 MET cc_start: 0.8270 (mpp) cc_final: 0.7712 (mmp) REVERT: A 518 LEU cc_start: 0.7394 (tp) cc_final: 0.7080 (tp) REVERT: A 733 LEU cc_start: 0.7004 (mt) cc_final: 0.6632 (mt) REVERT: B 616 LEU cc_start: 0.2453 (mm) cc_final: 0.1970 (mm) REVERT: C 65 CYS cc_start: 0.5224 (OUTLIER) cc_final: 0.3697 (t) REVERT: C 597 GLU cc_start: 0.4454 (mp0) cc_final: 0.2626 (mt-10) REVERT: D 145 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7152 (pttt) REVERT: D 154 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7601 (tt0) REVERT: D 375 MET cc_start: 0.7513 (tpp) cc_final: 0.6977 (mpp) REVERT: D 404 GLN cc_start: 0.7556 (tp40) cc_final: 0.7323 (tp-100) REVERT: F 300 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7131 (mtp) REVERT: F 510 MET cc_start: 0.1359 (mmm) cc_final: -0.1480 (ptp) REVERT: F 598 HIS cc_start: 0.4550 (OUTLIER) cc_final: 0.3902 (t-170) outliers start: 98 outliers final: 64 residues processed: 341 average time/residue: 0.4305 time to fit residues: 239.1266 Evaluate side-chains 319 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 249 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 1.9990 chunk 335 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 372 optimal weight: 20.0000 chunk 309 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 576 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 HIS ** E 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33043 Z= 0.233 Angle : 0.538 10.227 44678 Z= 0.269 Chirality : 0.040 0.222 5088 Planarity : 0.004 0.037 5505 Dihedral : 7.217 149.590 4455 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.74 % Allowed : 21.22 % Favored : 76.03 % 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: -0.51 (0.14), residues: 3846 helix: 0.49 (0.12), residues: 1885 sheet: -1.63 (0.28), residues: 424 loop : -0.86 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 170 HIS 0.006 0.001 HIS F 598 PHE 0.022 0.001 PHE C 728 TYR 0.016 0.001 TYR D 281 ARG 0.006 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 261 time to evaluate : 3.740 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 104 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.8575 (m90) REVERT: A 518 LEU cc_start: 0.7416 (tp) cc_final: 0.7139 (tp) REVERT: A 733 LEU cc_start: 0.6980 (mt) cc_final: 0.6603 (mt) REVERT: B 448 LEU cc_start: 0.4222 (OUTLIER) cc_final: 0.3737 (mm) REVERT: B 478 HIS cc_start: 0.4314 (m-70) cc_final: 0.4006 (m170) REVERT: B 616 LEU cc_start: 0.2536 (OUTLIER) cc_final: 0.2076 (mm) REVERT: D 145 LYS cc_start: 0.8482 (mmmt) cc_final: 0.7172 (pttt) REVERT: D 154 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7619 (tt0) REVERT: D 375 MET cc_start: 0.7551 (tpp) cc_final: 0.6994 (mpp) REVERT: D 404 GLN cc_start: 0.7513 (tp40) cc_final: 0.7258 (tp-100) REVERT: D 408 ASN cc_start: 0.7563 (m-40) cc_final: 0.6581 (p0) REVERT: F 300 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7241 (mtt) REVERT: F 510 MET cc_start: 0.1213 (mmm) cc_final: -0.1351 (ptp) REVERT: F 598 HIS cc_start: 0.4669 (OUTLIER) cc_final: 0.4035 (t70) outliers start: 99 outliers final: 68 residues processed: 343 average time/residue: 0.4269 time to fit residues: 240.7406 Evaluate side-chains 315 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 242 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain D residue 95 THR 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 280 CYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 208 optimal weight: 0.4980 chunk 371 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 66 ASN A 499 HIS ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN F 482 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 33043 Z= 0.363 Angle : 0.595 11.296 44678 Z= 0.300 Chirality : 0.042 0.197 5088 Planarity : 0.004 0.036 5505 Dihedral : 7.110 153.231 4455 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.05 % Allowed : 21.00 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3846 helix: 0.34 (0.12), residues: 1887 sheet: -1.63 (0.27), residues: 423 loop : -0.95 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 475 HIS 0.009 0.001 HIS E 499 PHE 0.027 0.002 PHE F 144 TYR 0.031 0.002 TYR A 689 ARG 0.004 0.000 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 249 time to evaluate : 3.830 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 104 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8643 (m90) REVERT: A 275 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8705 (t80) REVERT: A 433 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 434 MET cc_start: 0.8289 (mpp) cc_final: 0.7679 (mmp) REVERT: A 498 LEU cc_start: 0.8718 (tp) cc_final: 0.8443 (mt) REVERT: A 518 LEU cc_start: 0.7434 (tp) cc_final: 0.7166 (tp) REVERT: A 733 LEU cc_start: 0.6980 (mt) cc_final: 0.6584 (mt) REVERT: B 616 LEU cc_start: 0.2741 (OUTLIER) cc_final: 0.2507 (mm) REVERT: C 143 TRP cc_start: 0.7670 (OUTLIER) cc_final: 0.7265 (t60) REVERT: D 145 LYS cc_start: 0.8527 (mmmt) cc_final: 0.7255 (pttt) REVERT: D 154 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7616 (tt0) REVERT: D 375 MET cc_start: 0.7634 (tpp) cc_final: 0.6990 (mpp) REVERT: D 379 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7455 (mp) REVERT: D 404 GLN cc_start: 0.7489 (tp40) cc_final: 0.7090 (tp-100) REVERT: D 408 ASN cc_start: 0.7646 (m-40) cc_final: 0.6622 (p0) REVERT: F 300 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7226 (mtp) REVERT: F 510 MET cc_start: 0.1280 (mmm) cc_final: -0.1275 (ptp) REVERT: F 598 HIS cc_start: 0.4759 (OUTLIER) cc_final: 0.4000 (t-170) outliers start: 110 outliers final: 86 residues processed: 338 average time/residue: 0.4264 time to fit residues: 236.8758 Evaluate side-chains 330 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 236 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 0.4980 chunk 148 optimal weight: 0.6980 chunk 221 optimal weight: 0.0070 chunk 111 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 291 optimal weight: 20.0000 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 66 ASN A 576 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33043 Z= 0.147 Angle : 0.516 13.273 44678 Z= 0.257 Chirality : 0.039 0.185 5088 Planarity : 0.003 0.037 5505 Dihedral : 6.429 135.652 4455 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.02 % Allowed : 22.14 % Favored : 75.84 % 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: -0.33 (0.14), residues: 3846 helix: 0.62 (0.12), residues: 1876 sheet: -1.31 (0.29), residues: 393 loop : -0.86 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 145 HIS 0.005 0.001 HIS F 598 PHE 0.021 0.001 PHE B 443 TYR 0.028 0.001 TYR A 689 ARG 0.005 0.000 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 275 time to evaluate : 3.768 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 104 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8555 (m90) REVERT: A 275 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8663 (t80) REVERT: A 433 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 434 MET cc_start: 0.8347 (mpp) cc_final: 0.7785 (mmp) REVERT: A 498 LEU cc_start: 0.8755 (tp) cc_final: 0.8394 (mt) REVERT: A 733 LEU cc_start: 0.7021 (mt) cc_final: 0.6639 (mt) REVERT: D 20 LEU cc_start: 0.8828 (mp) cc_final: 0.8602 (mp) REVERT: D 145 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7229 (pttt) REVERT: D 154 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7566 (tt0) REVERT: D 308 TYR cc_start: 0.9232 (m-80) cc_final: 0.8992 (m-80) REVERT: D 375 MET cc_start: 0.7520 (tpp) cc_final: 0.7064 (mmm) REVERT: D 379 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7188 (mp) REVERT: D 404 GLN cc_start: 0.7464 (tp40) cc_final: 0.7210 (tp-100) REVERT: D 408 ASN cc_start: 0.7565 (m-40) cc_final: 0.6760 (p0) REVERT: F 300 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: F 510 MET cc_start: 0.1367 (mmm) cc_final: -0.0983 (ptp) REVERT: F 598 HIS cc_start: 0.4930 (OUTLIER) cc_final: 0.4146 (t70) outliers start: 73 outliers final: 47 residues processed: 336 average time/residue: 0.4255 time to fit residues: 233.4607 Evaluate side-chains 304 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 0.6980 chunk 355 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 345 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 327 optimal weight: 0.0870 chunk 344 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33043 Z= 0.176 Angle : 0.524 13.712 44678 Z= 0.260 Chirality : 0.040 0.335 5088 Planarity : 0.003 0.039 5505 Dihedral : 6.174 119.298 4455 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.72 % Allowed : 22.50 % Favored : 75.78 % 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: -0.29 (0.14), residues: 3846 helix: 0.65 (0.12), residues: 1879 sheet: -1.32 (0.29), residues: 393 loop : -0.81 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP E 475 HIS 0.006 0.001 HIS E 499 PHE 0.034 0.001 PHE D 390 TYR 0.027 0.001 TYR A 689 ARG 0.006 0.000 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 258 time to evaluate : 3.735 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 104 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8560 (m90) REVERT: A 275 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8661 (t80) REVERT: A 433 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 434 MET cc_start: 0.8352 (mpp) cc_final: 0.7789 (mmp) REVERT: A 498 LEU cc_start: 0.8754 (tp) cc_final: 0.8385 (mt) REVERT: A 733 LEU cc_start: 0.7093 (mt) cc_final: 0.6719 (mt) REVERT: B 428 LEU cc_start: 0.4186 (tt) cc_final: 0.3947 (mt) REVERT: B 592 ASN cc_start: 0.3458 (p0) cc_final: 0.1808 (m110) REVERT: D 20 LEU cc_start: 0.8821 (mp) cc_final: 0.8595 (mp) REVERT: D 145 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7246 (pttt) REVERT: D 154 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7557 (tt0) REVERT: D 308 TYR cc_start: 0.9240 (m-80) cc_final: 0.8981 (m-80) REVERT: D 375 MET cc_start: 0.7459 (tpp) cc_final: 0.7141 (mmm) REVERT: D 379 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7258 (mp) REVERT: D 404 GLN cc_start: 0.7455 (tp40) cc_final: 0.7190 (tp-100) REVERT: D 408 ASN cc_start: 0.7585 (m-40) cc_final: 0.6795 (p0) REVERT: F 300 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7248 (mtt) REVERT: F 510 MET cc_start: 0.1363 (mmm) cc_final: -0.0823 (ptp) REVERT: F 588 MET cc_start: -0.3290 (ptm) cc_final: -0.3751 (ttt) REVERT: F 598 HIS cc_start: 0.4946 (OUTLIER) cc_final: 0.4170 (t70) REVERT: F 701 GLU cc_start: 0.2838 (OUTLIER) cc_final: 0.2530 (pm20) outliers start: 62 outliers final: 48 residues processed: 310 average time/residue: 0.4244 time to fit residues: 216.7004 Evaluate side-chains 306 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 251 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.9980 chunk 365 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 383 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 66 ASN A 576 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33043 Z= 0.351 Angle : 0.588 15.673 44678 Z= 0.295 Chirality : 0.042 0.226 5088 Planarity : 0.004 0.039 5505 Dihedral : 6.611 117.306 4455 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.83 % Allowed : 22.39 % Favored : 75.78 % 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: -0.53 (0.14), residues: 3846 helix: 0.44 (0.12), residues: 1897 sheet: -1.46 (0.29), residues: 393 loop : -0.91 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 475 HIS 0.006 0.001 HIS F 598 PHE 0.036 0.002 PHE D 390 TYR 0.028 0.002 TYR A 689 ARG 0.006 0.000 ARG C 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 246 time to evaluate : 3.752 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: A 104 HIS cc_start: 0.9093 (OUTLIER) cc_final: 0.8619 (m90) REVERT: A 275 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8682 (t80) REVERT: A 433 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7334 (t80) REVERT: A 434 MET cc_start: 0.8381 (mpp) cc_final: 0.7788 (mmp) REVERT: A 733 LEU cc_start: 0.7000 (mt) cc_final: 0.6680 (mt) REVERT: D 145 LYS cc_start: 0.8558 (mmmt) cc_final: 0.7268 (pttt) REVERT: D 154 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7622 (tt0) REVERT: D 375 MET cc_start: 0.7612 (tpp) cc_final: 0.7315 (mmm) REVERT: D 379 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7409 (mp) REVERT: D 404 GLN cc_start: 0.7474 (tp40) cc_final: 0.7208 (tp-100) REVERT: D 408 ASN cc_start: 0.7375 (m-40) cc_final: 0.6730 (p0) REVERT: F 300 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7242 (mtp) REVERT: F 510 MET cc_start: 0.1412 (mmm) cc_final: -0.0724 (ptp) REVERT: F 588 MET cc_start: -0.3115 (ptm) cc_final: -0.3374 (ttp) REVERT: F 598 HIS cc_start: 0.4875 (OUTLIER) cc_final: 0.4091 (t70) REVERT: F 701 GLU cc_start: 0.2704 (OUTLIER) cc_final: 0.2403 (pm20) outliers start: 66 outliers final: 50 residues processed: 299 average time/residue: 0.4431 time to fit residues: 216.8999 Evaluate side-chains 297 residues out of total 3609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 240 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 753 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 783 VAL Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 281 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 499 HIS ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.220404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.170196 restraints weight = 52868.490| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.55 r_work: 0.3679 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33043 Z= 0.344 Angle : 0.590 16.804 44678 Z= 0.296 Chirality : 0.042 0.260 5088 Planarity : 0.004 0.038 5505 Dihedral : 6.751 101.628 4455 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.72 % Allowed : 22.64 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3846 helix: 0.36 (0.12), residues: 1903 sheet: -1.50 (0.29), residues: 393 loop : -0.98 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 475 HIS 0.006 0.001 HIS F 598 PHE 0.035 0.002 PHE D 390 TYR 0.026 0.002 TYR A 689 ARG 0.006 0.000 ARG C 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7765.81 seconds wall clock time: 141 minutes 49.85 seconds (8509.85 seconds total)