Starting phenix.real_space_refine on Fri Apr 12 01:07:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/04_2024/8h9e_34564_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/04_2024/8h9e_34564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/04_2024/8h9e_34564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/04_2024/8h9e_34564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/04_2024/8h9e_34564_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/04_2024/8h9e_34564_updated.pdb" } resolution = 2.53 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= 0.000 sd= 0.029 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 87 5.16 5 C 15234 2.51 5 N 4210 2.21 5 O 4665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 401": "OE1" <-> "OE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 398": "OE1" <-> "OE2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ASP 355": "OD1" <-> "OD2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 397": "OD1" <-> "OD2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "O TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 127": "OE1" <-> "OE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24214 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 623 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.09, per 1000 atoms: 0.54 Number of scatterers: 24214 At special positions: 0 Unit cell: (132.86, 124.1, 134.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 13 15.00 Mg 5 11.99 O 4665 8.00 N 4210 7.00 C 15234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.95 Conformation dependent library (CDL) restraints added in 4.1 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 23 sheets defined 43.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 191 removed outlier: 3.806A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 240 through 259 Proline residue: A 247 - end of helix removed outlier: 3.993A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.358A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 381 through 403 removed outlier: 3.994A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.668A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 190 removed outlier: 4.262A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 240 through 259 Proline residue: B 247 - end of helix removed outlier: 3.990A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.743A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.384A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 428 Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.914A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.738A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 240 through 259 Proline residue: C 247 - end of helix removed outlier: 4.128A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.788A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 399 removed outlier: 4.031A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 458 through 475 removed outlier: 3.515A pdb=" N ILE C 461 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 507 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 229 through 248 removed outlier: 4.897A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 288 through 298 removed outlier: 4.411A pdb=" N ARG E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 340 through 343 No H-bonds generated for 'chain 'E' and resid 340 through 343' Processing helix chain 'E' and resid 363 through 366 No H-bonds generated for 'chain 'E' and resid 363 through 366' Processing helix chain 'E' and resid 368 through 390 removed outlier: 3.582A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 428 removed outlier: 5.194A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR E 428 " --> pdb=" O GLU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 Processing helix chain 'E' and resid 457 through 459 No H-bonds generated for 'chain 'E' and resid 457 through 459' Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 165 through 176 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 4.939A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 274 removed outlier: 3.595A pdb=" N ALA F 273 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 288 through 298 removed outlier: 4.190A pdb=" N ARG F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 331 removed outlier: 4.558A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 344 Processing helix chain 'F' and resid 363 through 393 removed outlier: 7.794A pdb=" N SER F 368 " --> pdb=" O ASN F 364 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N GLU F 369 " --> pdb=" O ILE F 365 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 437 through 449 Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 466 through 476 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 229 through 248 removed outlier: 4.872A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 removed outlier: 5.062A pdb=" N ALA D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 323 through 331 removed outlier: 4.543A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N HIS D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 368 through 394 removed outlier: 4.177A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 401 through 417 Processing helix chain 'D' and resid 422 through 428 removed outlier: 3.796A pdb=" N GLU D 425 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL D 426 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 428 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 449 Processing helix chain 'D' and resid 457 through 460 Processing helix chain 'D' and resid 466 through 479 Processing helix chain 'G' and resid 3 through 31 Processing helix chain 'G' and resid 224 through 270 Processing helix chain 'O' and resid 13 through 27 Processing helix chain 'O' and resid 32 through 47 Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 62 through 75 Processing helix chain 'O' and resid 80 through 91 Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.552A pdb=" N GLN O 99 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 removed outlier: 4.120A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 158 No H-bonds generated for 'chain 'O' and resid 156 through 158' Processing helix chain 'O' and resid 175 through 187 Processing helix chain 'J' and resid 14 through 17 No H-bonds generated for 'chain 'J' and resid 14 through 17' Processing helix chain 'J' and resid 21 through 44 removed outlier: 3.948A pdb=" N ALA J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.920A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.087A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.367A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.549A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 324 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.610A pdb=" N LYS B 60 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 35 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.138A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.202A pdb=" N VAL B 108 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 231 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 324 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.714A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.526A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.089A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 349 through 351 removed outlier: 6.682A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 229 through 234 removed outlier: 8.729A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS C 263 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE C 202 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 265 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL C 204 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE C 266 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 324 " --> pdb=" O TYR C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.615A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE E 16 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.548A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 334 through 337 removed outlier: 8.392A pdb=" N ILE E 155 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER E 309 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU E 157 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN E 311 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.616A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 18 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE F 16 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.337A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 334 through 337 removed outlier: 7.445A pdb=" N ILE F 155 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER F 309 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU F 157 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN F 311 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY F 159 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE F 313 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR F 183 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE F 257 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 185 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP F 259 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA F 187 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.592A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 18 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN D 27 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE D 16 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.398A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 312 through 314 removed outlier: 5.994A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR D 336 " --> pdb=" O PHE D 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 218 through 223 removed outlier: 7.007A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER D 306 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU D 256 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR D 308 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE D 258 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 310 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 147 through 150 1024 hydrogen bonds defined for protein. 2796 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: 9.15 Time building geometry restraints manager: 10.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5119 1.33 - 1.45: 4927 1.45 - 1.57: 14323 1.57 - 1.69: 21 1.69 - 1.81: 167 Bond restraints: 24557 Sorted by residual: bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.457 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.284 0.090 1.00e-02 1.00e+04 8.01e+01 bond pdb=" C8 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.370 1.263 0.107 1.20e-02 6.94e+03 7.98e+01 ... (remaining 24552 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.94: 525 105.94 - 113.85: 14454 113.85 - 121.77: 13178 121.77 - 129.68: 4995 129.68 - 137.60: 61 Bond angle restraints: 33213 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.58 16.29 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.89 14.98 1.00e+00 1.00e+00 2.24e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 125.71 11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 125.74 11.09 1.00e+00 1.00e+00 1.23e+02 ... (remaining 33208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 14750 35.15 - 70.30: 283 70.30 - 105.45: 40 105.45 - 140.60: 0 140.60 - 175.75: 3 Dihedral angle restraints: 15076 sinusoidal: 6097 harmonic: 8979 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.76 -175.75 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 109.33 -169.33 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.99 -146.98 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 15073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2824 0.050 - 0.101: 848 0.101 - 0.151: 188 0.151 - 0.202: 7 0.202 - 0.252: 4 Chirality restraints: 3871 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE D 278 " pdb=" N ILE D 278 " pdb=" C ILE D 278 " pdb=" CB ILE D 278 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3868 not shown) Planarity restraints: 4292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 188 " 0.630 9.50e-02 1.11e+02 2.82e-01 4.87e+01 pdb=" NE ARG A 188 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 188 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 188 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 188 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.584 9.50e-02 1.11e+02 2.62e-01 4.18e+01 pdb=" NE ARG J 16 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 25 " -0.270 9.50e-02 1.11e+02 1.21e-01 9.02e+00 pdb=" NE ARG J 25 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG J 25 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG J 25 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 25 " -0.009 2.00e-02 2.50e+03 ... (remaining 4289 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 152 2.54 - 3.13: 19025 3.13 - 3.72: 37808 3.72 - 4.31: 58705 4.31 - 4.90: 94802 Nonbonded interactions: 210492 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.956 2.170 nonbonded pdb=" O1B ADP F 501 " pdb="MG MG F 502 " model vdw 2.048 2.170 nonbonded pdb=" O3G ATP B 601 " pdb="MG MG B 602 " model vdw 2.084 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 2.086 2.170 nonbonded pdb=" OG1 THR D 166 " pdb="MG MG D 502 " model vdw 2.097 2.170 ... (remaining 210487 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 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'C' and (resid 24 through 508 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 through 475)) } 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: 9.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 29.290 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 67.810 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.120 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.008 0.145 24557 Z= 0.546 Angle : 0.803 17.256 33213 Z= 0.515 Chirality : 0.049 0.252 3871 Planarity : 0.008 0.282 4292 Dihedral : 14.539 175.753 9336 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: -1.86 (0.13), residues: 3134 helix: -0.92 (0.12), residues: 1361 sheet: -0.96 (0.22), residues: 479 loop : -1.52 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 180 PHE 0.015 0.002 PHE F 444 TYR 0.012 0.002 TYR A 446 ARG 0.005 0.001 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.575 Fit side-chains REVERT: A 359 LYS cc_start: 0.8232 (mttt) cc_final: 0.7955 (mttm) REVERT: A 399 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7438 (tp30) REVERT: A 419 SER cc_start: 0.8511 (m) cc_final: 0.8303 (m) REVERT: A 488 LYS cc_start: 0.8627 (pttt) cc_final: 0.8295 (ptpt) REVERT: C 8 MET cc_start: 0.4229 (ptt) cc_final: 0.3757 (ptp) REVERT: D 212 LYS cc_start: 0.7863 (ptpp) cc_final: 0.7655 (ptpp) REVERT: D 470 VAL cc_start: 0.7787 (m) cc_final: 0.7579 (t) REVERT: O 69 LEU cc_start: 0.6587 (mm) cc_final: 0.6218 (mm) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 1.9512 time to fit residues: 919.3264 Evaluate side-chains 303 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.3980 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 0.0170 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 0.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 416 GLN A 492 GLN A 503 ASN B 78 ASN B 466 ASN C 208 GLN C 385 GLN C 503 ASN E 382 GLN F 115 GLN F 224 GLN F 249 GLN F 296 GLN F 331 HIS D 115 GLN D 201 HIS D 252 GLN D 266 GLN D 446 GLN D 458 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 ASN O 99 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24557 Z= 0.130 Angle : 0.485 7.707 33213 Z= 0.250 Chirality : 0.042 0.145 3871 Planarity : 0.004 0.046 4292 Dihedral : 7.854 149.807 3541 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.72 % Favored : 98.18 % Rotamer: Outliers : 1.64 % Allowed : 10.90 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: -0.16 (0.15), residues: 3134 helix: 0.60 (0.14), residues: 1352 sheet: -0.48 (0.22), residues: 514 loop : -0.57 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 454 PHE 0.015 0.001 PHE J 34 TYR 0.012 0.001 TYR F 245 ARG 0.008 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 352 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.8110 (mttt) cc_final: 0.7899 (mttm) REVERT: A 488 LYS cc_start: 0.8593 (pttt) cc_final: 0.8273 (ptpt) REVERT: B 455 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7773 (mmpt) REVERT: B 456 LEU cc_start: 0.8225 (mp) cc_final: 0.7975 (mp) REVERT: C 8 MET cc_start: 0.4185 (ptt) cc_final: 0.3715 (ptp) REVERT: C 497 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6878 (tt) REVERT: E 112 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7986 (mtpt) REVERT: E 249 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: E 415 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6902 (mpt180) REVERT: D 414 GLN cc_start: 0.7629 (tt0) cc_final: 0.7368 (tt0) REVERT: D 470 VAL cc_start: 0.7836 (m) cc_final: 0.7576 (t) REVERT: G 264 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7817 (mt-10) outliers start: 42 outliers final: 12 residues processed: 366 average time/residue: 1.6692 time to fit residues: 684.8684 Evaluate side-chains 325 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 309 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 96 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 306 optimal weight: 7.9990 chunk 252 optimal weight: 0.9980 chunk 281 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 475 GLN A 492 GLN B 78 ASN C 385 GLN C 503 ASN E 388 GLN E 445 GLN D 252 GLN D 458 GLN O 97 ASN J 41 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 24557 Z= 0.443 Angle : 0.605 9.261 33213 Z= 0.311 Chirality : 0.047 0.151 3871 Planarity : 0.005 0.053 4292 Dihedral : 8.260 148.137 3541 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 2.92 % Allowed : 11.72 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: -0.22 (0.15), residues: 3134 helix: 0.42 (0.14), residues: 1375 sheet: -0.41 (0.22), residues: 491 loop : -0.51 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 201 PHE 0.017 0.002 PHE F 444 TYR 0.018 0.002 TYR B 446 ARG 0.006 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 310 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 411 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7268 (p0) REVERT: A 488 LYS cc_start: 0.8633 (pttt) cc_final: 0.8308 (ptpt) REVERT: B 54 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6965 (tm-30) REVERT: B 355 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: B 455 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7822 (mmpt) REVERT: C 8 MET cc_start: 0.4204 (ptt) cc_final: 0.3720 (ptp) REVERT: C 497 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.6860 (tt) REVERT: C 498 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7200 (ttpp) REVERT: E 112 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8047 (mtpt) REVERT: E 249 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: E 415 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7024 (mpt90) REVERT: D 470 VAL cc_start: 0.7785 (m) cc_final: 0.7522 (t) REVERT: O 28 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.5698 (mptt) REVERT: O 126 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7347 (mt) outliers start: 75 outliers final: 26 residues processed: 349 average time/residue: 1.7751 time to fit residues: 693.2457 Evaluate side-chains 328 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 291 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain O residue 28 LYS Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 0.0470 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 301 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 492 GLN C 385 GLN C 503 ASN E 260 ASN E 388 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24557 Z= 0.184 Angle : 0.498 7.746 33213 Z= 0.255 Chirality : 0.042 0.147 3871 Planarity : 0.004 0.039 4292 Dihedral : 7.507 149.337 3541 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.53 % Favored : 98.40 % Rotamer: Outliers : 2.06 % Allowed : 13.82 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.27 (0.15), residues: 3134 helix: 0.83 (0.14), residues: 1376 sheet: -0.25 (0.23), residues: 493 loop : -0.21 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 471 PHE 0.014 0.001 PHE J 34 TYR 0.010 0.001 TYR O 59 ARG 0.006 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 315 time to evaluate : 2.992 Fit side-chains revert: symmetry clash REVERT: A 488 LYS cc_start: 0.8619 (pttt) cc_final: 0.8282 (ptpt) REVERT: B 455 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7794 (mmpt) REVERT: C 8 MET cc_start: 0.4171 (ptt) cc_final: 0.3380 (mmt) REVERT: C 475 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: C 497 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6916 (tt) REVERT: C 498 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7187 (ttpp) REVERT: E 112 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8000 (mtpt) REVERT: E 415 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6923 (mpt180) REVERT: D 458 GLN cc_start: 0.7738 (pm20) cc_final: 0.7466 (pm20) REVERT: D 470 VAL cc_start: 0.7808 (m) cc_final: 0.7511 (t) REVERT: G 264 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7884 (mt-10) REVERT: O 69 LEU cc_start: 0.6743 (mm) cc_final: 0.6313 (mm) outliers start: 53 outliers final: 16 residues processed: 349 average time/residue: 1.7500 time to fit residues: 685.3618 Evaluate side-chains 315 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 294 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 492 GLN C 503 ASN E 388 GLN E 445 GLN F 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24557 Z= 0.241 Angle : 0.516 8.059 33213 Z= 0.264 Chirality : 0.043 0.139 3871 Planarity : 0.004 0.040 4292 Dihedral : 7.510 152.540 3541 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.09 % Rotamer: Outliers : 2.22 % Allowed : 14.91 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.35 (0.15), residues: 3134 helix: 0.87 (0.14), residues: 1378 sheet: -0.21 (0.23), residues: 486 loop : -0.14 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 201 PHE 0.014 0.001 PHE J 34 TYR 0.021 0.001 TYR B 446 ARG 0.006 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 305 time to evaluate : 3.002 Fit side-chains REVERT: A 170 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: A 393 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: A 488 LYS cc_start: 0.8619 (pttt) cc_final: 0.8286 (ptpt) REVERT: B 355 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: B 426 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7310 (tp30) REVERT: B 455 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7791 (mmpt) REVERT: C 8 MET cc_start: 0.4165 (ptt) cc_final: 0.3405 (mmt) REVERT: C 426 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: C 475 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: C 497 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6903 (tt) REVERT: C 498 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7205 (ttpp) REVERT: E 112 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: E 249 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: E 415 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6987 (mpt180) REVERT: F 27 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: D 318 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: D 458 GLN cc_start: 0.7643 (pm20) cc_final: 0.7199 (pm20) REVERT: D 470 VAL cc_start: 0.7785 (m) cc_final: 0.7502 (t) REVERT: G 264 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7875 (mt-10) REVERT: O 69 LEU cc_start: 0.6743 (mm) cc_final: 0.6340 (mm) outliers start: 57 outliers final: 20 residues processed: 340 average time/residue: 1.7986 time to fit residues: 685.0776 Evaluate side-chains 325 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 293 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 492 GLN C 385 GLN C 503 ASN E 388 GLN E 445 GLN D 201 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24557 Z= 0.291 Angle : 0.541 8.351 33213 Z= 0.276 Chirality : 0.044 0.144 3871 Planarity : 0.004 0.041 4292 Dihedral : 7.646 155.133 3541 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 2.53 % Allowed : 14.91 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.32 (0.15), residues: 3134 helix: 0.80 (0.14), residues: 1385 sheet: -0.21 (0.23), residues: 486 loop : -0.11 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 454 PHE 0.016 0.002 PHE B 351 TYR 0.012 0.001 TYR O 170 ARG 0.007 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 297 time to evaluate : 2.804 Fit side-chains REVERT: A 393 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: A 411 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7178 (p0) REVERT: A 488 LYS cc_start: 0.8608 (pttt) cc_final: 0.8274 (ptpt) REVERT: B 54 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: B 144 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: B 355 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: B 392 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8375 (tm) REVERT: B 455 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7787 (mmpt) REVERT: B 465 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: C 8 MET cc_start: 0.4263 (ptt) cc_final: 0.3463 (mmt) REVERT: C 426 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: C 475 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: C 497 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6921 (tt) REVERT: C 498 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7217 (ttpp) REVERT: E 112 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7984 (mtpt) REVERT: E 249 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: E 415 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6957 (mpt180) REVERT: F 27 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: F 422 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7047 (mt0) REVERT: D 318 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: D 458 GLN cc_start: 0.7596 (pm20) cc_final: 0.7023 (tp40) REVERT: D 470 VAL cc_start: 0.7786 (m) cc_final: 0.7508 (t) REVERT: G 264 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7880 (mt-10) REVERT: O 36 GLU cc_start: 0.6452 (tt0) cc_final: 0.5713 (mt-10) REVERT: O 69 LEU cc_start: 0.6729 (mm) cc_final: 0.6387 (mm) REVERT: O 110 SER cc_start: 0.7524 (m) cc_final: 0.7083 (t) outliers start: 65 outliers final: 26 residues processed: 338 average time/residue: 1.7806 time to fit residues: 676.7166 Evaluate side-chains 330 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 287 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 254 optimal weight: 0.4980 chunk 168 optimal weight: 0.0020 chunk 300 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 48 GLN B 492 GLN C 385 GLN C 432 GLN C 503 ASN E 252 GLN E 388 GLN E 445 GLN ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 201 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24557 Z= 0.131 Angle : 0.477 8.127 33213 Z= 0.241 Chirality : 0.041 0.178 3871 Planarity : 0.003 0.037 4292 Dihedral : 6.889 153.982 3541 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Rotamer: Outliers : 1.99 % Allowed : 15.42 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3134 helix: 1.20 (0.14), residues: 1374 sheet: 0.02 (0.24), residues: 464 loop : 0.03 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 370 PHE 0.018 0.001 PHE E 427 TYR 0.010 0.001 TYR O 59 ARG 0.007 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 314 time to evaluate : 2.935 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6728 (mtp) cc_final: 0.6245 (mmt) REVERT: A 393 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: A 488 LYS cc_start: 0.8613 (pttt) cc_final: 0.8265 (ptpt) REVERT: B 144 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: B 355 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: B 392 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (tm) REVERT: B 426 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7282 (tp30) REVERT: B 455 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7770 (mmpt) REVERT: C 8 MET cc_start: 0.4143 (ptt) cc_final: 0.3387 (mmt) REVERT: C 426 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: C 475 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: C 497 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6935 (tt) REVERT: C 498 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7427 (ttmt) REVERT: E 112 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7975 (mtpt) REVERT: E 249 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7655 (mp10) REVERT: E 415 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6836 (mpt180) REVERT: F 27 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: D 318 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: D 470 VAL cc_start: 0.7822 (m) cc_final: 0.7513 (t) REVERT: G 264 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7827 (mt-10) REVERT: O 36 GLU cc_start: 0.6387 (tt0) cc_final: 0.5814 (mt-10) REVERT: O 69 LEU cc_start: 0.6749 (mm) cc_final: 0.6420 (mm) outliers start: 51 outliers final: 15 residues processed: 343 average time/residue: 1.7169 time to fit residues: 661.4955 Evaluate side-chains 329 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 301 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 492 GLN C 503 ASN E 252 GLN E 388 GLN E 445 GLN D 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24557 Z= 0.209 Angle : 0.507 9.595 33213 Z= 0.257 Chirality : 0.043 0.143 3871 Planarity : 0.004 0.054 4292 Dihedral : 7.083 154.905 3541 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.98 % Favored : 97.99 % Rotamer: Outliers : 1.91 % Allowed : 16.04 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.71 (0.15), residues: 3134 helix: 1.13 (0.14), residues: 1382 sheet: -0.05 (0.23), residues: 487 loop : 0.12 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 476 PHE 0.015 0.001 PHE B 351 TYR 0.022 0.001 TYR B 446 ARG 0.014 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 297 time to evaluate : 3.182 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6744 (mtp) cc_final: 0.6257 (mmt) REVERT: A 390 MET cc_start: 0.8750 (ttt) cc_final: 0.8488 (ttt) REVERT: A 393 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 54 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: B 144 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: B 195 GLU cc_start: 0.6874 (tp30) cc_final: 0.6505 (tp30) REVERT: B 355 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: B 426 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7316 (tp30) REVERT: B 455 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7764 (mmpt) REVERT: C 8 MET cc_start: 0.4191 (ptt) cc_final: 0.3400 (mmt) REVERT: C 426 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 475 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: C 497 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6959 (tt) REVERT: C 498 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7271 (ttpp) REVERT: E 112 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8006 (mtpt) REVERT: E 249 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: E 415 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6860 (mpt180) REVERT: F 27 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: D 318 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: D 470 VAL cc_start: 0.7835 (m) cc_final: 0.7527 (t) REVERT: O 69 LEU cc_start: 0.6775 (mm) cc_final: 0.6441 (mm) REVERT: O 153 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6691 (pttt) outliers start: 49 outliers final: 23 residues processed: 327 average time/residue: 1.7812 time to fit residues: 658.3646 Evaluate side-chains 338 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 301 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 492 GLN C 385 GLN C 432 GLN C 503 ASN E 388 GLN E 445 GLN D 201 HIS D 458 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24557 Z= 0.320 Angle : 0.563 10.244 33213 Z= 0.286 Chirality : 0.045 0.149 3871 Planarity : 0.004 0.041 4292 Dihedral : 7.553 157.207 3541 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.83 % Rotamer: Outliers : 1.99 % Allowed : 16.00 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 (0.15), residues: 3134 helix: 0.95 (0.14), residues: 1382 sheet: -0.09 (0.23), residues: 486 loop : 0.04 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 454 PHE 0.013 0.002 PHE J 34 TYR 0.015 0.002 TYR E 384 ARG 0.008 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 290 time to evaluate : 3.014 Fit side-chains REVERT: A 390 MET cc_start: 0.8800 (ttt) cc_final: 0.8533 (ttt) REVERT: A 393 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: A 411 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7089 (p0) REVERT: B 54 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: B 144 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: B 355 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: B 426 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7343 (tp30) REVERT: B 455 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7788 (mmpt) REVERT: C 8 MET cc_start: 0.4356 (ptt) cc_final: 0.3597 (mmt) REVERT: C 475 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: C 497 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6976 (tt) REVERT: C 498 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7236 (ttpp) REVERT: E 112 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7991 (mtpt) REVERT: E 249 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: E 415 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6923 (mpt180) REVERT: F 27 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: D 318 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: D 470 VAL cc_start: 0.7810 (m) cc_final: 0.7535 (t) REVERT: D 475 LYS cc_start: 0.7123 (tmmm) cc_final: 0.6892 (ttpt) REVERT: G 262 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8356 (tt) REVERT: O 69 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6413 (mm) REVERT: O 110 SER cc_start: 0.7384 (m) cc_final: 0.6972 (t) REVERT: O 153 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6728 (pttt) outliers start: 51 outliers final: 22 residues processed: 319 average time/residue: 1.8088 time to fit residues: 645.8401 Evaluate side-chains 319 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.5980 chunk 296 optimal weight: 20.0000 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 492 GLN C 432 GLN C 503 ASN E 388 GLN E 445 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24557 Z= 0.236 Angle : 0.537 11.290 33213 Z= 0.271 Chirality : 0.043 0.147 3871 Planarity : 0.004 0.039 4292 Dihedral : 7.380 157.035 3541 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Rotamer: Outliers : 1.95 % Allowed : 16.47 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 (0.15), residues: 3134 helix: 1.02 (0.14), residues: 1376 sheet: -0.07 (0.23), residues: 486 loop : 0.07 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 454 PHE 0.019 0.001 PHE B 351 TYR 0.018 0.001 TYR E 384 ARG 0.009 0.000 ARG C 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 288 time to evaluate : 2.980 Fit side-chains revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: A 411 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7075 (p0) REVERT: B 54 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: B 144 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: B 195 GLU cc_start: 0.6850 (tp30) cc_final: 0.6438 (tp30) REVERT: B 355 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: B 426 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7316 (tp30) REVERT: B 455 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7779 (mmpt) REVERT: C 8 MET cc_start: 0.4337 (ptt) cc_final: 0.3586 (mmt) REVERT: C 426 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: C 475 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: C 497 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6967 (tt) REVERT: C 498 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7271 (ttpp) REVERT: E 112 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7964 (mtpt) REVERT: E 249 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: E 415 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6902 (mpt180) REVERT: F 27 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: D 318 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: D 470 VAL cc_start: 0.7796 (m) cc_final: 0.7518 (t) REVERT: G 262 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8303 (tt) REVERT: O 56 LEU cc_start: 0.6217 (mm) cc_final: 0.5946 (mt) REVERT: O 69 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6437 (mm) REVERT: O 110 SER cc_start: 0.7317 (m) cc_final: 0.6922 (t) REVERT: O 153 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6733 (pttt) outliers start: 50 outliers final: 26 residues processed: 317 average time/residue: 1.8281 time to fit residues: 652.9519 Evaluate side-chains 326 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 283 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 4.9990 chunk 263 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 228 optimal weight: 0.0170 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 475 GLN A 492 GLN B 492 GLN C 385 GLN C 503 ASN E 252 GLN E 445 GLN ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.094114 restraints weight = 29324.164| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.79 r_work: 0.2969 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24557 Z= 0.139 Angle : 0.493 11.100 33213 Z= 0.247 Chirality : 0.042 0.137 3871 Planarity : 0.004 0.050 4292 Dihedral : 6.803 154.914 3541 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.79 % Favored : 98.18 % Rotamer: Outliers : 1.56 % Allowed : 16.82 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.91 (0.15), residues: 3134 helix: 1.29 (0.14), residues: 1372 sheet: 0.10 (0.24), residues: 464 loop : 0.19 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 476 PHE 0.020 0.001 PHE B 468 TYR 0.022 0.001 TYR B 446 ARG 0.014 0.000 ARG F 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11026.06 seconds wall clock time: 198 minutes 54.59 seconds (11934.59 seconds total)