Starting phenix.real_space_refine on Tue Mar 19 11:12:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9l_34572/03_2024/8h9l_34572_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9l_34572/03_2024/8h9l_34572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9l_34572/03_2024/8h9l_34572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9l_34572/03_2024/8h9l_34572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9l_34572/03_2024/8h9l_34572_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9l_34572/03_2024/8h9l_34572_updated.pdb" } resolution = 2.61 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= 0.028 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 85 5.16 5 C 15081 2.51 5 N 4170 2.21 5 O 4609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 24": "OD1" <-> "OD2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" 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 181": "OD1" <-> "OD2" Residue "A GLU 195": "OE1" <-> "OE2" 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 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 ASP 494": "OD1" <-> "OD2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" 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 440": "OE1" <-> "OE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 333": "OD1" <-> "OD2" 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 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" 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 GLU 30": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 297": "OE1" <-> "OE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E ASP 403": "OD1" <-> "OD2" 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 PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 132": "OE1" <-> "OE2" 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 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 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 PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 362": "OD1" <-> "OD2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 397": "OD1" <-> "OD2" 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 ASP 29": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 344": "OE1" <-> "OE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 425": "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 5": "OD1" <-> "OD2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J GLU 40": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 172": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23963 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} 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: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} 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: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} 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: "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: 12.45, per 1000 atoms: 0.52 Number of scatterers: 23963 At special positions: 0 Unit cell: (125.56, 123.37, 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 85 16.00 P 13 15.00 Mg 5 11.99 O 4609 8.00 N 4170 7.00 C 15081 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: 9.92 Conformation dependent library (CDL) restraints added in 4.5 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 129 helices and 23 sheets defined 43.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... 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: 3.802A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 3.995A 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: 4.421A 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 399 removed outlier: 3.946A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' 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 428 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.624A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 506 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: 4.314A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.698A 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 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 240 through 260 Proline residue: B 247 - end of helix removed outlier: 4.058A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (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 296 through 306 removed outlier: 4.330A pdb=" N PHE B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 300 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 301 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG B 304 " --> 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 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.627A 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 449 Processing helix chain 'B' and resid 458 through 474 removed outlier: 4.512A pdb=" N THR B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (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 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.740A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) 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 258 Proline residue: C 247 - end of helix removed outlier: 4.020A 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: 4.057A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.359A 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: 3.594A 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: 4.398A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (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: 4.976A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.959A 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 288 through 298 removed outlier: 4.623A 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 344 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: 4.167A 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: 5.272A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR E 428 " --> pdb=" O GLU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 448 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 175 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 4.897A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 274 removed outlier: 3.763A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU F 274 " --> 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 296 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: 4.611A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.621A 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 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 368 through 394 removed outlier: 4.843A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.259A 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 422 through 427 removed outlier: 3.826A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL F 426 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 427 " --> pdb=" O ALA F 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 422 through 427' Processing helix chain 'F' and resid 437 through 449 Processing helix chain 'F' and resid 457 through 460 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 204 Processing helix chain 'D' and resid 229 through 248 removed outlier: 4.957A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 removed outlier: 3.620A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU D 274 " --> 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 298 removed outlier: 4.443A pdb=" N ARG D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) 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: 4.529A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 343 No H-bonds generated for 'chain 'D' and resid 340 through 343' Processing helix chain 'D' and resid 363 through 366 No H-bonds generated for 'chain 'D' and resid 363 through 366' Processing helix chain 'D' and resid 368 through 394 removed outlier: 4.013A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 417 Processing helix chain 'D' and resid 425 through 428 No H-bonds generated for 'chain 'D' and resid 425 through 428' Processing helix chain 'D' and resid 437 through 449 Processing helix chain 'D' and resid 466 through 479 Processing helix chain 'G' and resid 3 through 30 Processing helix chain 'G' and resid 224 through 270 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 42 removed outlier: 3.721A pdb=" N GLU J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 29 removed outlier: 3.735A pdb=" N GLN O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 46 Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 62 through 74 Processing helix chain 'O' and resid 80 through 92 Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.791A pdb=" N GLN O 99 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 removed outlier: 3.661A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.352A 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 sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.561A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA A 93 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLU A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 91 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.073A 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: 6.604A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.070A 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: 6.715A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 324 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.546A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B 93 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.134A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.739A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.653A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 324 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.455A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.540A 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: 4.248A 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 352 removed outlier: 6.659A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.835A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.919A 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: 7.797A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU C 324 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.710A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.615A 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: 4.243A 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: 8.476A pdb=" N ILE E 155 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER E 309 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU E 157 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 6.284A 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: 6.618A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.700A 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: 4.186A 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: 7.502A pdb=" N ILE F 155 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER F 309 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU F 157 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN F 311 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY F 159 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE F 313 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR F 183 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N PHE F 257 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL F 185 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP F 259 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.295A 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: 6.675A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 18 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLN D 27 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.779A 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: 4.202A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 157 through 159 Processing sheet with id= V, first strand: chain 'D' and resid 218 through 223 removed outlier: 7.054A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL D 185 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 255 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA D 187 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE D 257 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL D 189 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP D 259 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER D 306 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 256 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR D 308 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE D 258 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL D 310 " --> pdb=" O ILE D 258 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'O' and resid 147 through 154 removed outlier: 3.504A pdb=" N GLU O 151 " --> pdb=" O CYS O 118 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2898 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: 8.58 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4574 1.32 - 1.44: 5299 1.44 - 1.56: 14250 1.56 - 1.69: 21 1.69 - 1.81: 163 Bond restraints: 24307 Sorted by residual: bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.12e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.453 -0.116 1.10e-02 8.26e+03 1.12e+02 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.282 0.092 1.00e-02 1.00e+04 8.51e+01 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.283 0.091 1.00e-02 1.00e+04 8.34e+01 ... (remaining 24302 not shown) Histogram of bond angle deviations from ideal: 97.27 - 105.24: 470 105.24 - 113.21: 13819 113.21 - 121.18: 12497 121.18 - 129.14: 6022 129.14 - 137.11: 70 Bond angle restraints: 32878 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.84 17.03 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.23 15.64 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.77 14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 124.91 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " pdb=" C8 ATP B 601 " ideal model delta sigma weight residual 105.72 115.08 -9.36 1.00e+00 1.00e+00 8.77e+01 ... (remaining 32873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.36: 14381 29.36 - 58.71: 470 58.71 - 88.07: 61 88.07 - 117.43: 5 117.43 - 146.78: 2 Dihedral angle restraints: 14919 sinusoidal: 6035 harmonic: 8884 Sorted by residual: 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 86.78 -146.78 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 171.03 128.97 1 2.00e+01 2.50e-03 3.91e+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 48.07 -108.07 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2486 0.049 - 0.099: 1078 0.099 - 0.148: 248 0.148 - 0.197: 11 0.197 - 0.247: 4 Chirality restraints: 3827 Sorted by residual: 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 -2.43 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE C 121 " pdb=" N ILE C 121 " pdb=" C ILE C 121 " pdb=" CB ILE C 121 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 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 -2.45 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 3824 not shown) Planarity restraints: 4250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.712 9.50e-02 1.11e+02 3.19e-01 6.21e+01 pdb=" NE ARG J 16 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.73e+00 pdb=" C ASN D 174 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN D 174 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN D 175 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 279 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C PRO D 279 " -0.036 2.00e-02 2.50e+03 pdb=" O PRO D 279 " 0.014 2.00e-02 2.50e+03 pdb=" N SER D 280 " 0.012 2.00e-02 2.50e+03 ... (remaining 4247 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 73 2.41 - 3.03: 14532 3.03 - 3.65: 35738 3.65 - 4.28: 60288 4.28 - 4.90: 97486 Nonbonded interactions: 208117 Sorted by model distance: nonbonded pdb=" OG1 THR D 166 " pdb="MG MG D 502 " model vdw 1.782 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 1.890 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.975 2.170 nonbonded pdb=" OG1 THR F 166 " pdb="MG MG F 502 " model vdw 2.052 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 2.082 2.170 ... (remaining 208112 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' } 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: 11.960 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: 30.940 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 66.330 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.150 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:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.011 0.144 24307 Z= 0.714 Angle : 0.874 17.033 32878 Z= 0.538 Chirality : 0.054 0.247 3827 Planarity : 0.007 0.319 4250 Dihedral : 14.631 146.783 9241 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: -2.29 (0.13), residues: 3102 helix: -1.50 (0.12), residues: 1333 sheet: -1.23 (0.22), residues: 479 loop : -1.46 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 201 PHE 0.025 0.002 PHE J 34 TYR 0.015 0.002 TYR A 452 ARG 0.009 0.001 ARG F 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 2.761 Fit side-chains REVERT: B 498 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7529 (tptt) REVERT: C 124 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7702 (mttm) REVERT: C 386 VAL cc_start: 0.8129 (m) cc_final: 0.7800 (p) REVERT: C 457 GLU cc_start: 0.7607 (tt0) cc_final: 0.7312 (mt-10) REVERT: C 471 HIS cc_start: 0.6210 (t70) cc_final: 0.5501 (t-170) REVERT: D 390 ILE cc_start: 0.8420 (mt) cc_final: 0.8212 (mm) REVERT: D 475 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7425 (tmtt) REVERT: O 107 THR cc_start: 0.8274 (t) cc_final: 0.8026 (p) REVERT: O 111 VAL cc_start: 0.7598 (p) cc_final: 0.7271 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 1.7650 time to fit residues: 760.1670 Evaluate side-chains 289 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.4980 chunk 234 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 396 GLN A 475 GLN A 477 GLN A 503 ASN B 48 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN C 208 GLN C 215 GLN C 385 GLN C 432 GLN E 370 HIS F 27 GLN F 174 ASN F 180 HIS F 197 ASN F 296 GLN F 331 HIS F 458 GLN D 180 HIS D 201 HIS D 266 GLN D 422 GLN G 15 ASN O 92 ASN O 97 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24307 Z= 0.158 Angle : 0.501 10.093 32878 Z= 0.257 Chirality : 0.042 0.152 3827 Planarity : 0.004 0.042 4250 Dihedral : 7.697 141.826 3506 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.42 % Allowed : 10.52 % Favored : 88.07 % 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 (0.14), residues: 3102 helix: 0.31 (0.14), residues: 1328 sheet: -0.80 (0.22), residues: 484 loop : -0.73 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 476 PHE 0.017 0.001 PHE J 34 TYR 0.012 0.001 TYR C 397 ARG 0.006 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 343 time to evaluate : 2.705 Fit side-chains REVERT: B 67 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: B 498 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7499 (tptt) REVERT: C 26 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7776 (mp0) REVERT: C 124 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7689 (mttm) REVERT: C 224 ASP cc_start: 0.7550 (t0) cc_final: 0.7313 (t0) REVERT: C 457 GLU cc_start: 0.7640 (tt0) cc_final: 0.7416 (mt-10) REVERT: C 471 HIS cc_start: 0.6050 (t70) cc_final: 0.5451 (t-170) REVERT: C 496 LYS cc_start: 0.6863 (tptt) cc_final: 0.6452 (tttt) REVERT: F 112 LYS cc_start: 0.8257 (mttt) cc_final: 0.8024 (mttp) REVERT: F 210 ASN cc_start: 0.8394 (t0) cc_final: 0.8077 (t0) REVERT: F 397 ASP cc_start: 0.7391 (m-30) cc_final: 0.7142 (m-30) REVERT: D 249 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: D 475 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7356 (tmtt) REVERT: O 111 VAL cc_start: 0.7583 (p) cc_final: 0.7272 (t) outliers start: 36 outliers final: 13 residues processed: 361 average time/residue: 1.6133 time to fit residues: 654.9162 Evaluate side-chains 314 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 299 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 249 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 303 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 405 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN F 27 GLN F 430 HIS F 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 24307 Z= 0.473 Angle : 0.621 10.730 32878 Z= 0.317 Chirality : 0.048 0.168 3827 Planarity : 0.004 0.044 4250 Dihedral : 8.355 150.241 3506 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 2.99 % Allowed : 12.45 % Favored : 84.56 % 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: -0.26 (0.15), residues: 3102 helix: 0.51 (0.14), residues: 1323 sheet: -0.65 (0.22), residues: 503 loop : -0.54 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 476 PHE 0.021 0.002 PHE J 34 TYR 0.016 0.002 TYR B 446 ARG 0.004 0.001 ARG F 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 298 time to evaluate : 2.933 Fit side-chains REVERT: A 101 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: B 67 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: B 475 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: B 498 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7546 (tptt) REVERT: C 124 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7739 (mttm) REVERT: C 224 ASP cc_start: 0.7660 (t0) cc_final: 0.7380 (t0) REVERT: C 457 GLU cc_start: 0.7568 (tt0) cc_final: 0.7335 (mt-10) REVERT: C 471 HIS cc_start: 0.6050 (t70) cc_final: 0.5457 (t-170) REVERT: E 15 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7435 (ptm-80) REVERT: E 29 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6778 (p0) REVERT: E 122 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: E 439 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: D 249 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: D 475 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7390 (tmtt) REVERT: O 107 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7917 (p) REVERT: O 111 VAL cc_start: 0.7555 (p) cc_final: 0.7177 (m) outliers start: 76 outliers final: 39 residues processed: 341 average time/residue: 1.6515 time to fit residues: 632.8277 Evaluate side-chains 329 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 281 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 439 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.0570 chunk 211 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 267 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN C 215 GLN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN O 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24307 Z= 0.148 Angle : 0.477 9.325 32878 Z= 0.242 Chirality : 0.042 0.152 3827 Planarity : 0.003 0.038 4250 Dihedral : 7.221 146.847 3506 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.16 % Rotamer: Outliers : 2.01 % Allowed : 14.30 % Favored : 83.69 % 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: 0.45 (0.15), residues: 3102 helix: 1.20 (0.14), residues: 1327 sheet: -0.42 (0.23), residues: 482 loop : -0.24 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 180 PHE 0.017 0.001 PHE A 406 TYR 0.011 0.001 TYR O 170 ARG 0.006 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 320 time to evaluate : 2.348 Fit side-chains REVERT: B 498 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7493 (tptt) REVERT: C 124 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7694 (mttm) REVERT: C 146 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7710 (tmm) REVERT: C 471 HIS cc_start: 0.5907 (t70) cc_final: 0.5339 (t-170) REVERT: C 496 LYS cc_start: 0.6798 (tptt) cc_final: 0.6274 (tttm) REVERT: F 112 LYS cc_start: 0.8268 (mttt) cc_final: 0.8027 (mttp) REVERT: F 249 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: F 400 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7713 (p) REVERT: D 475 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7401 (tmtt) REVERT: G 241 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: O 15 GLU cc_start: 0.7058 (mp0) cc_final: 0.6815 (mp0) REVERT: O 107 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7950 (p) REVERT: O 111 VAL cc_start: 0.7571 (p) cc_final: 0.7206 (t) outliers start: 51 outliers final: 21 residues processed: 349 average time/residue: 1.5107 time to fit residues: 595.7303 Evaluate side-chains 322 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 296 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 7.9990 chunk 169 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24307 Z= 0.339 Angle : 0.556 11.227 32878 Z= 0.283 Chirality : 0.045 0.182 3827 Planarity : 0.004 0.041 4250 Dihedral : 7.798 154.463 3506 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 2.56 % Allowed : 14.97 % Favored : 82.47 % 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: 0.42 (0.15), residues: 3102 helix: 1.14 (0.14), residues: 1323 sheet: -0.42 (0.23), residues: 503 loop : -0.20 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 370 PHE 0.019 0.002 PHE J 34 TYR 0.018 0.002 TYR B 446 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 292 time to evaluate : 2.851 Fit side-chains REVERT: B 67 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: B 475 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: B 498 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7410 (tptt) REVERT: C 124 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7719 (mttm) REVERT: C 471 HIS cc_start: 0.5930 (t70) cc_final: 0.5365 (t-170) REVERT: E 15 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7409 (ptm-80) REVERT: F 112 LYS cc_start: 0.8257 (mttt) cc_final: 0.8026 (mttp) REVERT: F 210 ASN cc_start: 0.8288 (t0) cc_final: 0.8030 (t0) REVERT: F 249 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: D 385 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7863 (mttt) REVERT: D 475 LYS cc_start: 0.7663 (ttpt) cc_final: 0.7384 (tmtt) REVERT: O 15 GLU cc_start: 0.7097 (mp0) cc_final: 0.6853 (mp0) REVERT: O 107 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7947 (p) REVERT: O 111 VAL cc_start: 0.7582 (p) cc_final: 0.7226 (t) outliers start: 65 outliers final: 38 residues processed: 329 average time/residue: 1.5927 time to fit residues: 590.4326 Evaluate side-chains 326 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 282 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 298 optimal weight: 20.0000 chunk 248 optimal weight: 0.7980 chunk 138 optimal weight: 0.0020 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS A 432 GLN A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 42 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 24307 Z= 0.146 Angle : 0.479 10.486 32878 Z= 0.243 Chirality : 0.042 0.146 3827 Planarity : 0.003 0.038 4250 Dihedral : 7.038 151.724 3506 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.10 % Rotamer: Outliers : 2.21 % Allowed : 15.64 % Favored : 82.16 % 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: 0.81 (0.15), residues: 3102 helix: 1.52 (0.14), residues: 1326 sheet: -0.30 (0.23), residues: 494 loop : -0.04 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 476 PHE 0.020 0.001 PHE C 468 TYR 0.011 0.001 TYR O 170 ARG 0.007 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 316 time to evaluate : 2.498 Fit side-chains REVERT: B 301 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 373 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6946 (mmt90) REVERT: B 498 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7378 (tptt) REVERT: C 124 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7689 (mttm) REVERT: E 224 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7184 (mm-40) REVERT: F 112 LYS cc_start: 0.8241 (mttt) cc_final: 0.8024 (mttp) REVERT: F 249 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: F 400 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7735 (p) REVERT: D 170 MET cc_start: 0.8060 (mmt) cc_final: 0.7678 (mmt) REVERT: D 475 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7385 (tmtt) REVERT: O 107 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7900 (p) REVERT: O 111 VAL cc_start: 0.7582 (p) cc_final: 0.7254 (t) outliers start: 56 outliers final: 26 residues processed: 350 average time/residue: 1.6242 time to fit residues: 646.4444 Evaluate side-chains 325 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 293 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 0.0370 chunk 169 optimal weight: 0.6980 chunk 251 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 186 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN C 432 GLN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24307 Z= 0.158 Angle : 0.486 12.622 32878 Z= 0.245 Chirality : 0.042 0.145 3827 Planarity : 0.003 0.038 4250 Dihedral : 6.884 149.809 3506 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 1.81 % Allowed : 16.74 % Favored : 81.45 % 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: 0.99 (0.15), residues: 3102 helix: 1.66 (0.14), residues: 1330 sheet: -0.25 (0.23), residues: 497 loop : 0.09 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 370 PHE 0.017 0.001 PHE J 34 TYR 0.021 0.001 TYR B 446 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.807 Fit side-chains REVERT: B 301 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 498 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7400 (tptt) REVERT: C 124 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7692 (mttm) REVERT: F 249 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: F 400 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7714 (p) REVERT: D 170 MET cc_start: 0.8020 (mmt) cc_final: 0.7655 (mmt) REVERT: D 431 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6839 (tpt) REVERT: D 475 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7388 (tmtt) REVERT: O 111 VAL cc_start: 0.7587 (p) cc_final: 0.7263 (t) REVERT: O 139 LYS cc_start: 0.6793 (ptmm) cc_final: 0.6084 (tptp) outliers start: 46 outliers final: 29 residues processed: 334 average time/residue: 1.5137 time to fit residues: 571.9193 Evaluate side-chains 327 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 294 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 1.9990 chunk 118 optimal weight: 0.0060 chunk 177 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24307 Z= 0.166 Angle : 0.489 11.675 32878 Z= 0.248 Chirality : 0.042 0.143 3827 Planarity : 0.003 0.038 4250 Dihedral : 6.817 146.178 3506 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 16.74 % Favored : 81.49 % 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: 1.05 (0.15), residues: 3102 helix: 1.70 (0.15), residues: 1330 sheet: -0.20 (0.23), residues: 497 loop : 0.13 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 454 PHE 0.026 0.001 PHE C 468 TYR 0.012 0.001 TYR B 433 ARG 0.007 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 311 time to evaluate : 2.858 Fit side-chains REVERT: B 301 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8927 (tp) REVERT: B 486 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6661 (t0) REVERT: B 498 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7399 (tptt) REVERT: C 124 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7697 (mttm) REVERT: C 471 HIS cc_start: 0.5576 (t70) cc_final: 0.5358 (t-170) REVERT: F 249 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: F 400 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7734 (p) REVERT: D 170 MET cc_start: 0.7996 (mmt) cc_final: 0.7642 (mmt) REVERT: D 431 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6797 (tpt) REVERT: D 475 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7396 (tmtt) REVERT: G 241 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: O 136 THR cc_start: 0.7332 (m) cc_final: 0.7031 (p) REVERT: O 139 LYS cc_start: 0.6776 (ptmm) cc_final: 0.6263 (tptp) outliers start: 45 outliers final: 29 residues processed: 337 average time/residue: 1.5126 time to fit residues: 581.3962 Evaluate side-chains 326 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 291 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 277 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 276 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24307 Z= 0.283 Angle : 0.540 11.237 32878 Z= 0.274 Chirality : 0.044 0.155 3827 Planarity : 0.004 0.039 4250 Dihedral : 7.298 149.127 3506 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 1.97 % Allowed : 16.82 % Favored : 81.21 % 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: 0.84 (0.15), residues: 3102 helix: 1.49 (0.14), residues: 1326 sheet: -0.28 (0.23), residues: 497 loop : 0.06 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 454 PHE 0.017 0.001 PHE J 34 TYR 0.019 0.001 TYR B 446 ARG 0.006 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 289 time to evaluate : 2.808 Fit side-chains revert: symmetry clash REVERT: B 373 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6980 (mmt90) REVERT: B 486 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6590 (t0) REVERT: B 498 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7411 (tptt) REVERT: C 124 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7727 (mttm) REVERT: C 471 HIS cc_start: 0.5632 (t70) cc_final: 0.5415 (t-170) REVERT: F 249 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: D 431 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6924 (tpt) REVERT: D 475 LYS cc_start: 0.7685 (ttpt) cc_final: 0.7416 (tmtt) REVERT: G 241 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: O 139 LYS cc_start: 0.6773 (ptmm) cc_final: 0.6345 (tptp) outliers start: 50 outliers final: 33 residues processed: 314 average time/residue: 1.5833 time to fit residues: 560.8360 Evaluate side-chains 319 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 204 optimal weight: 0.5980 chunk 307 optimal weight: 7.9990 chunk 283 optimal weight: 0.1980 chunk 245 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 189 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN E 224 GLN F 27 GLN F 201 HIS F 458 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24307 Z= 0.138 Angle : 0.482 11.328 32878 Z= 0.243 Chirality : 0.042 0.154 3827 Planarity : 0.003 0.037 4250 Dihedral : 6.693 142.657 3506 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.54 % Allowed : 17.41 % Favored : 81.06 % 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: 1.11 (0.15), residues: 3102 helix: 1.72 (0.15), residues: 1332 sheet: -0.12 (0.23), residues: 505 loop : 0.16 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 454 PHE 0.030 0.001 PHE C 468 TYR 0.012 0.001 TYR O 170 ARG 0.007 0.000 ARG A 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 302 time to evaluate : 2.831 Fit side-chains revert: symmetry clash REVERT: B 486 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6619 (t0) REVERT: B 496 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7570 (tttp) REVERT: B 498 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7448 (tptt) REVERT: C 124 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7690 (mttm) REVERT: C 471 HIS cc_start: 0.5516 (t70) cc_final: 0.5068 (t-90) REVERT: F 249 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: F 400 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7738 (p) REVERT: D 170 MET cc_start: 0.8021 (mmt) cc_final: 0.7678 (mmt) REVERT: D 431 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6776 (tpt) REVERT: D 475 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7393 (tmtt) REVERT: G 241 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: O 15 GLU cc_start: 0.7078 (pt0) cc_final: 0.6686 (tt0) REVERT: O 139 LYS cc_start: 0.6732 (ptmm) cc_final: 0.6292 (tptp) outliers start: 39 outliers final: 28 residues processed: 326 average time/residue: 1.5326 time to fit residues: 570.0569 Evaluate side-chains 324 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.0030 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 overall best weight: 2.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN C 78 ASN E 210 ASN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098193 restraints weight = 31605.569| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.71 r_work: 0.3053 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24307 Z= 0.328 Angle : 0.569 11.022 32878 Z= 0.288 Chirality : 0.045 0.298 3827 Planarity : 0.004 0.039 4250 Dihedral : 7.406 146.463 3506 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 1.61 % Allowed : 17.41 % Favored : 80.98 % 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: 0.81 (0.15), residues: 3102 helix: 1.43 (0.14), residues: 1333 sheet: -0.28 (0.23), residues: 497 loop : 0.06 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 454 PHE 0.020 0.002 PHE A 406 TYR 0.019 0.002 TYR B 446 ARG 0.007 0.000 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9990.56 seconds wall clock time: 177 minutes 35.58 seconds (10655.58 seconds total)