Starting phenix.real_space_refine on Tue Mar 19 10:59:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9i_34568/03_2024/8h9i_34568_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9i_34568/03_2024/8h9i_34568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9i_34568/03_2024/8h9i_34568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9i_34568/03_2024/8h9i_34568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9i_34568/03_2024/8h9i_34568_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9i_34568/03_2024/8h9i_34568_updated.pdb" } resolution = 2.77 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= 0.023 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 88 5.16 5 C 15079 2.51 5 N 4158 2.21 5 O 4618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 96": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "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 GLU 292": "OE1" <-> "OE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 248": "OD1" <-> "OD2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E ASP 352": "OD1" <-> "OD2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ASP 248": "OD1" <-> "OD2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 277": "NH1" <-> "NH2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 340": "NH1" <-> "NH2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F GLU 478": "OE1" <-> "OE2" Residue "F GLU 479": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 76": "OE1" <-> "OE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D PHE 158": "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 TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 247": "NH1" <-> "NH2" 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 ASP 318": "OD1" <-> "OD2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ASP 362": "OD1" <-> "OD2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 389": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 468": "OE1" <-> "OE2" 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: 23961 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 Chain: "A" 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: "B" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3522 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 441} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 623 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "D" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3482 Classifications: {'peptide': 460} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 434} Chain breaks: 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: "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: "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: 12.86, per 1000 atoms: 0.54 Number of scatterers: 23961 At special positions: 0 Unit cell: (121.91, 128.48, 133.59, 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 88 16.00 P 13 15.00 Mg 5 11.99 O 4618 8.00 N 4158 7.00 C 15079 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: 10.26 Conformation dependent library (CDL) restraints added in 4.6 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 25 sheets defined 42.3% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.722A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 260 Proline residue: C 247 - end of helix removed outlier: 3.979A 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: 4.411A 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 355 through 358 No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 403 removed outlier: 4.337A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE C 403 " --> pdb=" O GLU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 458 through 474 removed outlier: 4.808A pdb=" N THR C 462 " --> 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 '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: 4.334A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.631A 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 259 Proline residue: A 247 - end of helix removed outlier: 3.930A 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 296 through 306 removed outlier: 4.454A pdb=" N PHE A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 301 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG A 304 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.819A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 474 removed outlier: 4.641A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 5.280A 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 9 through 12 No H-bonds generated for 'chain 'B' and resid 9 through 12' 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: 3.806A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) 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: 4.002A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.871A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.979A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 474 removed outlier: 4.979A pdb=" N THR B 462 " --> 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 507 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 166 through 179 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 229 through 250 removed outlier: 4.858A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.681A pdb=" N MET E 295 " --> pdb=" O ASP E 291 " (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 329 Processing helix chain 'E' and resid 340 through 344 Processing helix chain 'E' and resid 367 through 393 removed outlier: 4.249A pdb=" N ILE E 393 " --> pdb=" O ASP E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 416 Processing helix chain 'E' and resid 423 through 425 No H-bonds generated for 'chain 'E' and resid 423 through 425' Processing helix chain 'E' and resid 437 through 449 Processing helix chain 'E' and resid 466 through 475 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 179 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 5.103A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 275 removed outlier: 3.821A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) 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: 4.420A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N HIS F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.642A pdb=" N LEU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 394 removed outlier: 4.543A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.139A 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 428 removed outlier: 3.795A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL F 426 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR F 428 " --> pdb=" O GLU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 449 Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 466 through 479 Processing helix chain 'G' and resid 3 through 31 Processing helix chain 'G' and resid 224 through 270 Processing helix chain 'O' and resid 13 through 28 removed outlier: 3.942A pdb=" N LYS O 28 " --> pdb=" O SER O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 46 Processing helix chain 'O' and resid 49 through 56 Processing helix chain 'O' and resid 62 through 75 Processing helix chain 'O' and resid 80 through 91 Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.561A pdb=" N GLN O 99 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 141 removed outlier: 3.577A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 187 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 178 Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 229 through 248 removed outlier: 4.948A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 removed outlier: 4.706A 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 296 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 323 through 331 removed outlier: 4.444A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.372A 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 368 through 393 removed outlier: 3.811A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 401 through 416 Processing helix chain 'D' and resid 437 through 448 Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 466 through 479 Processing sheet with id= A, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.703A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.117A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.123A pdb=" N VAL C 108 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL C 231 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS C 263 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE C 202 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU C 265 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL C 204 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE C 266 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 349 through 352 removed outlier: 6.830A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.556A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.000A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.003A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.694A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 324 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.388A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 38 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 35 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.962A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 349 through 352 removed outlier: 7.049A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 229 through 234 removed outlier: 8.646A pdb=" N ILE B 230 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS B 263 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ILE B 202 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 265 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL B 204 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 267 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE B 206 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP B 269 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 324 " --> pdb=" O TYR B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.588A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.090A 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: 6.069A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.538A 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: 3.996A 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 336 removed outlier: 3.552A pdb=" N GLY E 156 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ILE E 155 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER E 309 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU E 157 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 6.772A 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: 6.750A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 18 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.429A 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: 4.202A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 157 through 159 Processing sheet with id= S, first strand: chain 'F' and resid 218 through 223 removed outlier: 6.989A pdb=" N SER F 184 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL F 221 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE F 186 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY F 223 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY F 188 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER F 306 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU F 256 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR F 308 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE F 258 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL F 310 " --> pdb=" O ILE F 258 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 147 through 151 removed outlier: 3.596A pdb=" N VAL O 120 " --> pdb=" O GLU O 151 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.681A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 18 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN D 27 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE D 16 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.915A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 134 through 136 removed outlier: 4.363A pdb=" N GLU D 134 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 157 through 159 Processing sheet with id= Y, first strand: chain 'D' and resid 218 through 223 removed outlier: 7.124A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER D 306 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU D 256 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 308 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE D 258 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL D 310 " --> pdb=" O ILE D 258 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2769 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: 8.54 Time building geometry restraints manager: 11.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5972 1.33 - 1.45: 3971 1.45 - 1.57: 14167 1.57 - 1.69: 21 1.69 - 1.81: 169 Bond restraints: 24300 Sorted by residual: bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.462 -0.125 1.10e-02 8.26e+03 1.28e+02 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 1.458 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.283 0.091 1.00e-02 1.00e+04 8.32e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.00e-02 1.00e+04 7.87e+01 ... (remaining 24295 not shown) Histogram of bond angle deviations from ideal: 98.64 - 106.34: 626 106.34 - 114.04: 14438 114.04 - 121.74: 12632 121.74 - 129.43: 5116 129.43 - 137.13: 63 Bond angle restraints: 32875 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 139.87 121.72 18.15 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 123.53 16.34 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 125.02 14.85 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.88 12.95 1.00e+00 1.00e+00 1.68e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 124.96 11.87 1.00e+00 1.00e+00 1.41e+02 ... (remaining 32870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 14532 32.36 - 64.72: 345 64.72 - 97.08: 47 97.08 - 129.43: 1 129.43 - 161.79: 1 Dihedral angle restraints: 14926 sinusoidal: 6030 harmonic: 8896 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 138.20 161.79 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 61.42 -121.42 1 2.00e+01 2.50e-03 3.65e+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 32.51 -92.51 1 2.00e+01 2.50e-03 2.51e+01 ... (remaining 14923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2862 0.050 - 0.101: 794 0.101 - 0.151: 175 0.151 - 0.201: 9 0.201 - 0.252: 3 Chirality restraints: 3843 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.58e+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 -2.44 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3840 not shown) Planarity restraints: 4244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 174 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ASN F 174 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN F 174 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN F 175 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 417 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LEU E 417 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU E 417 " 0.015 2.00e-02 2.50e+03 pdb=" N SER E 418 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASN D 174 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN D 174 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN D 175 " 0.013 2.00e-02 2.50e+03 ... (remaining 4241 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 190 2.54 - 3.13: 19057 3.13 - 3.72: 36886 3.72 - 4.31: 56547 4.31 - 4.90: 92890 Nonbonded interactions: 205570 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.946 2.170 nonbonded pdb=" O1B ATP A 601 " pdb="MG MG A 602 " model vdw 1.971 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.033 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.069 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 2.124 2.170 ... (remaining 205565 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 508 or resid 601 through 602)) selection = (chain 'C' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 477)) selection = (chain 'E' and (resid 12 through 420 or resid 431 through 477)) selection = (chain 'F' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 420 or resid 43 \ 1 through 477)) } 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: 21.470 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: 0.000 Extract box with map and model: 28.950 Check model and map are aligned: 1.130 Set scattering table: 0.000 Process input model: 66.590 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.130 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.007 0.143 24300 Z= 0.486 Angle : 0.798 18.154 32875 Z= 0.514 Chirality : 0.047 0.252 3843 Planarity : 0.004 0.041 4244 Dihedral : 14.435 161.794 9238 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -2.77 (0.13), residues: 3105 helix: -1.56 (0.12), residues: 1333 sheet: -1.63 (0.20), residues: 492 loop : -2.06 (0.15), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 370 PHE 0.011 0.002 PHE E 264 TYR 0.019 0.001 TYR O 170 ARG 0.008 0.000 ARG E 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 195 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6947 (tp30) REVERT: C 463 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8304 (ttmt) REVERT: C 484 ARG cc_start: 0.7034 (ttt-90) cc_final: 0.6686 (ttm170) REVERT: A 96 ASP cc_start: 0.8239 (p0) cc_final: 0.7936 (p0) REVERT: A 351 PHE cc_start: 0.7941 (m-80) cc_final: 0.7423 (t80) REVERT: A 362 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6590 (mtt90) REVERT: A 422 VAL cc_start: 0.6951 (t) cc_final: 0.6593 (m) REVERT: A 446 TYR cc_start: 0.7713 (t80) cc_final: 0.7359 (t80) REVERT: B 89 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8389 (mtmt) REVERT: F 408 SER cc_start: 0.7877 (m) cc_final: 0.7666 (p) REVERT: F 422 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7593 (tm-30) REVERT: G 229 MET cc_start: 0.7431 (ttp) cc_final: 0.7210 (ptm) REVERT: G 260 LYS cc_start: 0.8719 (tttt) cc_final: 0.8500 (tttp) REVERT: O 33 GLU cc_start: 0.7083 (pt0) cc_final: 0.6608 (pm20) REVERT: O 37 LYS cc_start: 0.7216 (tptm) cc_final: 0.6700 (tppt) REVERT: O 134 LEU cc_start: 0.7772 (tp) cc_final: 0.7465 (mp) REVERT: O 186 MET cc_start: 0.5992 (ptp) cc_final: 0.5474 (pp-130) REVERT: D 59 SER cc_start: 0.8979 (m) cc_final: 0.8752 (p) REVERT: D 149 TYR cc_start: 0.6360 (m-10) cc_final: 0.6126 (m-10) REVERT: D 180 HIS cc_start: 0.7594 (t-90) cc_final: 0.7379 (t-90) REVERT: D 248 ASP cc_start: 0.7190 (m-30) cc_final: 0.6841 (m-30) REVERT: D 462 MET cc_start: 0.5792 (mmt) cc_final: 0.5526 (mmt) outliers start: 0 outliers final: 1 residues processed: 415 average time/residue: 1.5411 time to fit residues: 721.4534 Evaluate side-chains 294 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 380 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN C 396 GLN A 396 GLN A 432 GLN A 471 HIS B 172 GLN B 385 GLN B 466 ASN E 378 GLN E 382 GLN E 419 GLN E 446 GLN F 133 GLN F 180 HIS F 266 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN O 84 ASN O 92 ASN O 112 HIS D 133 GLN D 201 HIS D 210 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24300 Z= 0.183 Angle : 0.523 8.025 32875 Z= 0.267 Chirality : 0.043 0.210 3843 Planarity : 0.004 0.035 4244 Dihedral : 7.504 127.978 3507 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 1.85 % Allowed : 10.88 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3105 helix: -0.16 (0.14), residues: 1335 sheet: -0.98 (0.22), residues: 488 loop : -1.45 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 370 PHE 0.025 0.001 PHE D 262 TYR 0.015 0.001 TYR O 170 ARG 0.007 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 330 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7642 (mmp80) REVERT: C 195 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6918 (tp30) REVERT: C 415 GLN cc_start: 0.6652 (mt0) cc_final: 0.6448 (mt0) REVERT: C 425 THR cc_start: 0.8825 (t) cc_final: 0.8598 (m) REVERT: C 484 ARG cc_start: 0.7063 (ttt-90) cc_final: 0.6772 (ttm170) REVERT: A 96 ASP cc_start: 0.8098 (p0) cc_final: 0.7783 (p0) REVERT: A 351 PHE cc_start: 0.7964 (m-80) cc_final: 0.7434 (t80) REVERT: A 362 ARG cc_start: 0.7557 (mtt180) cc_final: 0.6558 (mtt180) REVERT: A 422 VAL cc_start: 0.6912 (t) cc_final: 0.6553 (m) REVERT: A 446 TYR cc_start: 0.7536 (t80) cc_final: 0.7135 (t80) REVERT: B 8 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6120 (mpm) REVERT: B 89 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8399 (mtmt) REVERT: E 227 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: E 442 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7644 (ttpt) REVERT: F 170 MET cc_start: 0.8669 (tpp) cc_final: 0.8369 (mmt) REVERT: F 217 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7445 (mttp) REVERT: F 249 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: F 422 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7569 (tm-30) REVERT: G 229 MET cc_start: 0.7410 (ttp) cc_final: 0.7190 (ptm) REVERT: G 260 LYS cc_start: 0.8733 (tttt) cc_final: 0.8518 (tttp) REVERT: O 33 GLU cc_start: 0.7116 (pt0) cc_final: 0.6609 (pm20) REVERT: O 37 LYS cc_start: 0.7312 (tptm) cc_final: 0.6882 (tppt) REVERT: O 134 LEU cc_start: 0.7828 (tp) cc_final: 0.7493 (mp) REVERT: O 186 MET cc_start: 0.5911 (ptp) cc_final: 0.5352 (pp-130) REVERT: D 248 ASP cc_start: 0.7105 (m-30) cc_final: 0.6777 (m-30) REVERT: D 259 ASP cc_start: 0.8276 (t0) cc_final: 0.7942 (t0) outliers start: 47 outliers final: 18 residues processed: 361 average time/residue: 1.4547 time to fit residues: 602.7161 Evaluate side-chains 301 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 279 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 234 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 304 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 475 GLN B 466 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN D 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24300 Z= 0.265 Angle : 0.538 7.926 32875 Z= 0.274 Chirality : 0.044 0.182 3843 Planarity : 0.004 0.036 4244 Dihedral : 7.344 120.355 3505 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 2.79 % Allowed : 13.05 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -0.70 (0.15), residues: 3105 helix: 0.31 (0.14), residues: 1330 sheet: -0.74 (0.22), residues: 494 loop : -1.08 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 370 PHE 0.025 0.001 PHE D 262 TYR 0.020 0.001 TYR B 446 ARG 0.005 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 298 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 195 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6861 (tp30) REVERT: C 415 GLN cc_start: 0.6595 (mt0) cc_final: 0.6364 (mt0) REVERT: C 425 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8597 (m) REVERT: C 465 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: C 484 ARG cc_start: 0.7090 (ttt-90) cc_final: 0.6737 (ttm-80) REVERT: A 96 ASP cc_start: 0.8109 (p0) cc_final: 0.7809 (p0) REVERT: A 226 MET cc_start: 0.9066 (tpt) cc_final: 0.8471 (tpt) REVERT: A 351 PHE cc_start: 0.7718 (m-80) cc_final: 0.7377 (t80) REVERT: A 353 GLU cc_start: 0.7569 (tt0) cc_final: 0.7365 (tt0) REVERT: A 362 ARG cc_start: 0.7610 (mtt180) cc_final: 0.6629 (mtt180) REVERT: A 415 GLN cc_start: 0.6164 (pt0) cc_final: 0.5939 (pm20) REVERT: A 422 VAL cc_start: 0.7018 (t) cc_final: 0.6636 (m) REVERT: A 476 HIS cc_start: 0.6779 (m-70) cc_final: 0.6469 (m-70) REVERT: A 482 THR cc_start: 0.7814 (t) cc_final: 0.7606 (t) REVERT: B 8 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6076 (mpm) REVERT: B 89 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8392 (mtmt) REVERT: B 195 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: E 227 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: E 431 MET cc_start: 0.8044 (mmm) cc_final: 0.7647 (mtm) REVERT: F 170 MET cc_start: 0.8772 (tpp) cc_final: 0.8493 (mmt) REVERT: F 217 LYS cc_start: 0.7925 (ptpp) cc_final: 0.7496 (mttp) REVERT: F 249 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: F 422 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7602 (tm-30) REVERT: G 260 LYS cc_start: 0.8726 (tttt) cc_final: 0.8503 (tttp) REVERT: O 33 GLU cc_start: 0.7196 (pt0) cc_final: 0.6630 (pm20) REVERT: O 37 LYS cc_start: 0.7347 (tptm) cc_final: 0.6889 (tppt) REVERT: O 42 VAL cc_start: 0.7037 (t) cc_final: 0.6724 (m) REVERT: O 134 LEU cc_start: 0.7836 (tp) cc_final: 0.7533 (mp) REVERT: O 186 MET cc_start: 0.6018 (ptp) cc_final: 0.5483 (pp-130) REVERT: D 170 MET cc_start: 0.6562 (tpp) cc_final: 0.6340 (mmm) REVERT: D 248 ASP cc_start: 0.7096 (m-30) cc_final: 0.6782 (m-30) REVERT: D 290 THR cc_start: 0.6432 (t) cc_final: 0.6041 (p) REVERT: D 462 MET cc_start: 0.6250 (mmt) cc_final: 0.6039 (mmt) outliers start: 71 outliers final: 34 residues processed: 345 average time/residue: 1.3954 time to fit residues: 551.0141 Evaluate side-chains 316 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 268 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 475 GLN B 466 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24300 Z= 0.225 Angle : 0.521 8.735 32875 Z= 0.264 Chirality : 0.043 0.190 3843 Planarity : 0.004 0.035 4244 Dihedral : 7.157 121.976 3505 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 2.63 % Allowed : 14.93 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3105 helix: 0.61 (0.14), residues: 1329 sheet: -0.52 (0.23), residues: 483 loop : -0.93 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 370 PHE 0.022 0.001 PHE D 262 TYR 0.021 0.001 TYR B 446 ARG 0.008 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 299 time to evaluate : 2.570 Fit side-chains revert: symmetry clash REVERT: C 143 ARG cc_start: 0.7866 (tpp-160) cc_final: 0.7643 (mmp80) REVERT: C 415 GLN cc_start: 0.6523 (mt0) cc_final: 0.6281 (mt0) REVERT: C 425 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8584 (m) REVERT: C 465 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: C 473 VAL cc_start: 0.7105 (OUTLIER) cc_final: 0.6876 (t) REVERT: C 484 ARG cc_start: 0.7041 (ttt-90) cc_final: 0.6828 (ttt-90) REVERT: A 96 ASP cc_start: 0.8111 (p0) cc_final: 0.7809 (p0) REVERT: A 226 MET cc_start: 0.9048 (tpt) cc_final: 0.8525 (tpt) REVERT: A 351 PHE cc_start: 0.7703 (m-80) cc_final: 0.7324 (t80) REVERT: A 362 ARG cc_start: 0.7615 (mtt180) cc_final: 0.6610 (mtt90) REVERT: A 422 VAL cc_start: 0.7030 (t) cc_final: 0.6644 (m) REVERT: A 476 HIS cc_start: 0.6771 (m-70) cc_final: 0.6485 (m-70) REVERT: B 8 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6060 (mpm) REVERT: B 54 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: B 195 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: E 227 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: E 431 MET cc_start: 0.8035 (mmm) cc_final: 0.7717 (mtm) REVERT: F 170 MET cc_start: 0.8788 (tpp) cc_final: 0.8529 (mmt) REVERT: F 217 LYS cc_start: 0.7992 (ptpp) cc_final: 0.7557 (mttp) REVERT: F 253 ASP cc_start: 0.7845 (m-30) cc_final: 0.7593 (m-30) REVERT: F 422 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7582 (tm-30) REVERT: G 260 LYS cc_start: 0.8747 (tttt) cc_final: 0.8535 (tttp) REVERT: O 33 GLU cc_start: 0.7237 (pt0) cc_final: 0.6608 (pm20) REVERT: O 37 LYS cc_start: 0.7327 (tptm) cc_final: 0.6925 (tppt) REVERT: O 42 VAL cc_start: 0.7048 (t) cc_final: 0.6730 (m) REVERT: O 134 LEU cc_start: 0.7840 (tp) cc_final: 0.7560 (mp) REVERT: O 186 MET cc_start: 0.6089 (ptp) cc_final: 0.5531 (pp-130) REVERT: D 248 ASP cc_start: 0.7067 (m-30) cc_final: 0.6772 (m-30) REVERT: D 259 ASP cc_start: 0.8201 (t0) cc_final: 0.7989 (t0) REVERT: D 290 THR cc_start: 0.6384 (t) cc_final: 0.6009 (p) outliers start: 67 outliers final: 33 residues processed: 342 average time/residue: 1.4185 time to fit residues: 556.1551 Evaluate side-chains 312 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 475 GLN B 432 GLN B 466 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24300 Z= 0.307 Angle : 0.557 9.816 32875 Z= 0.282 Chirality : 0.044 0.214 3843 Planarity : 0.004 0.037 4244 Dihedral : 7.333 123.740 3505 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 3.14 % Allowed : 15.32 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3105 helix: 0.60 (0.14), residues: 1332 sheet: -0.47 (0.23), residues: 484 loop : -0.87 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 370 PHE 0.025 0.001 PHE C 464 TYR 0.023 0.002 TYR A 397 ARG 0.007 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 288 time to evaluate : 2.786 Fit side-chains revert: symmetry clash REVERT: C 425 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8610 (m) REVERT: C 465 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: C 473 VAL cc_start: 0.7108 (OUTLIER) cc_final: 0.6894 (t) REVERT: C 484 ARG cc_start: 0.7061 (ttt-90) cc_final: 0.6833 (ttt-90) REVERT: A 226 MET cc_start: 0.9024 (tpt) cc_final: 0.8443 (tpt) REVERT: A 351 PHE cc_start: 0.7574 (m-80) cc_final: 0.7307 (t80) REVERT: A 362 ARG cc_start: 0.7684 (mtt180) cc_final: 0.6686 (mtt90) REVERT: A 482 THR cc_start: 0.7788 (t) cc_final: 0.7543 (t) REVERT: B 8 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6018 (mpm) REVERT: B 54 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: B 195 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: E 227 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: E 431 MET cc_start: 0.8029 (mmm) cc_final: 0.7722 (mtm) REVERT: F 170 MET cc_start: 0.8793 (tpp) cc_final: 0.8538 (mmt) REVERT: F 217 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7680 (mttp) REVERT: F 422 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7607 (tm-30) REVERT: G 260 LYS cc_start: 0.8747 (tttt) cc_final: 0.8521 (tttp) REVERT: O 33 GLU cc_start: 0.7245 (pt0) cc_final: 0.6571 (pm20) REVERT: O 37 LYS cc_start: 0.7348 (tptm) cc_final: 0.6908 (tppt) REVERT: O 42 VAL cc_start: 0.7029 (t) cc_final: 0.6702 (m) REVERT: O 134 LEU cc_start: 0.7834 (tp) cc_final: 0.7589 (mp) REVERT: O 186 MET cc_start: 0.6092 (ptp) cc_final: 0.5529 (pp-130) REVERT: D 145 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5733 (tp) REVERT: D 248 ASP cc_start: 0.7075 (m-30) cc_final: 0.6745 (m-30) REVERT: D 259 ASP cc_start: 0.8317 (t0) cc_final: 0.8029 (t0) REVERT: D 479 GLU cc_start: 0.4117 (OUTLIER) cc_final: 0.3815 (mp0) outliers start: 80 outliers final: 43 residues processed: 342 average time/residue: 1.3097 time to fit residues: 516.0756 Evaluate side-chains 320 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 268 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.0050 chunk 269 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 175 optimal weight: 0.0370 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.8874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 HIS C 415 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN B 466 ASN F 388 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24300 Z= 0.169 Angle : 0.504 10.458 32875 Z= 0.255 Chirality : 0.042 0.160 3843 Planarity : 0.003 0.038 4244 Dihedral : 6.821 121.995 3505 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 2.40 % Allowed : 17.05 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.02 (0.15), residues: 3105 helix: 0.88 (0.15), residues: 1341 sheet: -0.29 (0.24), residues: 483 loop : -0.70 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 370 PHE 0.018 0.001 PHE D 262 TYR 0.027 0.001 TYR F 371 ARG 0.006 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 293 time to evaluate : 3.049 Fit side-chains revert: symmetry clash REVERT: C 473 VAL cc_start: 0.7026 (OUTLIER) cc_final: 0.6817 (t) REVERT: A 62 MET cc_start: 0.8685 (ttm) cc_final: 0.8448 (ttt) REVERT: A 226 MET cc_start: 0.9016 (tpt) cc_final: 0.8554 (tpt) REVERT: A 362 ARG cc_start: 0.7605 (mtt180) cc_final: 0.6659 (mtt90) REVERT: A 466 ASN cc_start: 0.8067 (m-40) cc_final: 0.7741 (m110) REVERT: A 498 LYS cc_start: 0.7881 (ptmt) cc_final: 0.7377 (pttm) REVERT: B 8 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6072 (mpm) REVERT: B 83 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7693 (mtpp) REVERT: E 227 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: E 431 MET cc_start: 0.7995 (mmm) cc_final: 0.7733 (mtm) REVERT: E 442 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7694 (ttpt) REVERT: F 170 MET cc_start: 0.8790 (tpp) cc_final: 0.8570 (mmt) REVERT: F 217 LYS cc_start: 0.7998 (ptpp) cc_final: 0.7538 (mttp) REVERT: F 422 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7591 (tm-30) REVERT: G 260 LYS cc_start: 0.8726 (tttt) cc_final: 0.8507 (tttp) REVERT: O 37 LYS cc_start: 0.7312 (tptm) cc_final: 0.6925 (tppt) REVERT: O 42 VAL cc_start: 0.7096 (t) cc_final: 0.6765 (m) REVERT: O 134 LEU cc_start: 0.7757 (tp) cc_final: 0.7499 (mp) REVERT: O 186 MET cc_start: 0.6100 (ptp) cc_final: 0.5539 (pp-130) REVERT: D 145 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5749 (tp) REVERT: D 203 MET cc_start: 0.8541 (mtt) cc_final: 0.8322 (mtt) REVERT: D 259 ASP cc_start: 0.8248 (t0) cc_final: 0.7950 (t0) outliers start: 61 outliers final: 32 residues processed: 331 average time/residue: 1.3868 time to fit residues: 528.5210 Evaluate side-chains 313 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 275 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN B 503 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24300 Z= 0.377 Angle : 0.594 11.105 32875 Z= 0.300 Chirality : 0.046 0.261 3843 Planarity : 0.004 0.040 4244 Dihedral : 7.383 124.662 3505 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.91 % Allowed : 17.60 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -0.19 (0.15), residues: 3105 helix: 0.66 (0.14), residues: 1342 sheet: -0.37 (0.23), residues: 484 loop : -0.77 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 370 PHE 0.030 0.002 PHE C 464 TYR 0.028 0.002 TYR F 461 ARG 0.005 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 278 time to evaluate : 2.621 Fit side-chains revert: symmetry clash REVERT: C 473 VAL cc_start: 0.7018 (OUTLIER) cc_final: 0.6810 (t) REVERT: C 484 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6576 (ttt-90) REVERT: A 226 MET cc_start: 0.9019 (tpt) cc_final: 0.8487 (tpt) REVERT: A 351 PHE cc_start: 0.7535 (m-80) cc_final: 0.7255 (t80) REVERT: A 362 ARG cc_start: 0.7761 (mtt180) cc_final: 0.6777 (mtt90) REVERT: A 466 ASN cc_start: 0.8086 (m-40) cc_final: 0.7768 (m110) REVERT: B 8 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6166 (mpm) REVERT: B 54 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: B 83 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7747 (mtpp) REVERT: B 195 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: B 496 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7532 (mmtm) REVERT: E 227 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: E 431 MET cc_start: 0.8042 (mmm) cc_final: 0.7751 (mtm) REVERT: F 170 MET cc_start: 0.8798 (tpp) cc_final: 0.8552 (mmt) REVERT: F 217 LYS cc_start: 0.8159 (ptpp) cc_final: 0.7704 (mttp) REVERT: F 402 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6654 (tp30) REVERT: F 422 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7623 (tm-30) REVERT: G 260 LYS cc_start: 0.8789 (tttt) cc_final: 0.8551 (tttp) REVERT: O 37 LYS cc_start: 0.7325 (tptm) cc_final: 0.6856 (tppt) REVERT: O 134 LEU cc_start: 0.7737 (tp) cc_final: 0.7537 (mp) REVERT: O 186 MET cc_start: 0.6060 (ptp) cc_final: 0.5483 (pp-130) REVERT: D 145 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5751 (tp) REVERT: D 203 MET cc_start: 0.8541 (mtt) cc_final: 0.8190 (mtt) REVERT: D 259 ASP cc_start: 0.8392 (t0) cc_final: 0.8057 (t0) REVERT: D 479 GLU cc_start: 0.4040 (OUTLIER) cc_final: 0.3828 (mt-10) outliers start: 74 outliers final: 44 residues processed: 327 average time/residue: 1.4228 time to fit residues: 531.3940 Evaluate side-chains 310 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 10 GLN Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 203 optimal weight: 0.2980 chunk 147 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 234 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 466 ASN B 503 ASN E 458 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24300 Z= 0.165 Angle : 0.518 11.822 32875 Z= 0.261 Chirality : 0.042 0.218 3843 Planarity : 0.003 0.044 4244 Dihedral : 6.799 122.291 3505 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 2.00 % Allowed : 18.78 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.14 (0.15), residues: 3105 helix: 0.94 (0.15), residues: 1342 sheet: -0.25 (0.24), residues: 483 loop : -0.59 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 476 PHE 0.016 0.001 PHE D 262 TYR 0.023 0.001 TYR B 446 ARG 0.007 0.000 ARG E 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 282 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8680 (ttm) cc_final: 0.8470 (ttt) REVERT: A 218 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7594 (tttt) REVERT: A 351 PHE cc_start: 0.7506 (m-80) cc_final: 0.7170 (t80) REVERT: A 362 ARG cc_start: 0.7676 (mtt180) cc_final: 0.6649 (mtt90) REVERT: A 466 ASN cc_start: 0.8118 (m-40) cc_final: 0.7805 (m110) REVERT: B 8 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6151 (mpm) REVERT: B 83 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7715 (mtpp) REVERT: B 195 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: E 227 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: E 431 MET cc_start: 0.8024 (mmm) cc_final: 0.7760 (mtm) REVERT: E 442 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7684 (ttpt) REVERT: F 30 GLU cc_start: 0.7579 (pm20) cc_final: 0.7379 (pm20) REVERT: F 170 MET cc_start: 0.8798 (tpp) cc_final: 0.8581 (mmt) REVERT: F 171 GLU cc_start: 0.7444 (tp30) cc_final: 0.7182 (tp30) REVERT: F 217 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7537 (mttp) REVERT: F 422 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7545 (tm-30) REVERT: G 260 LYS cc_start: 0.8743 (tttt) cc_final: 0.8505 (tttp) REVERT: O 37 LYS cc_start: 0.7215 (tptm) cc_final: 0.6830 (tppt) REVERT: O 134 LEU cc_start: 0.7723 (tp) cc_final: 0.7512 (mp) REVERT: O 186 MET cc_start: 0.6098 (ptp) cc_final: 0.5533 (pp-130) REVERT: D 145 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5723 (tp) REVERT: D 203 MET cc_start: 0.8539 (mtt) cc_final: 0.8163 (mtt) REVERT: D 259 ASP cc_start: 0.8260 (t0) cc_final: 0.7976 (t0) outliers start: 51 outliers final: 30 residues processed: 317 average time/residue: 1.4178 time to fit residues: 518.4972 Evaluate side-chains 307 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 270 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 278 optimal weight: 0.1980 chunk 167 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 251 optimal weight: 0.5980 chunk 263 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN B 503 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24300 Z= 0.154 Angle : 0.513 12.499 32875 Z= 0.255 Chirality : 0.042 0.225 3843 Planarity : 0.003 0.047 4244 Dihedral : 6.471 121.970 3505 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 1.69 % Allowed : 19.02 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.30 (0.15), residues: 3105 helix: 1.07 (0.15), residues: 1344 sheet: -0.19 (0.24), residues: 489 loop : -0.48 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 476 PHE 0.037 0.001 PHE C 464 TYR 0.028 0.001 TYR F 371 ARG 0.006 0.000 ARG E 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 288 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8667 (ttm) cc_final: 0.8449 (ttt) REVERT: A 218 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7605 (tttt) REVERT: A 351 PHE cc_start: 0.7520 (m-80) cc_final: 0.7156 (t80) REVERT: A 362 ARG cc_start: 0.7628 (mtt180) cc_final: 0.6676 (mtt90) REVERT: A 466 ASN cc_start: 0.8084 (m-40) cc_final: 0.7777 (m110) REVERT: B 195 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: E 227 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: E 431 MET cc_start: 0.7996 (mmm) cc_final: 0.7776 (mtm) REVERT: E 442 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: F 170 MET cc_start: 0.8819 (tpp) cc_final: 0.8609 (mmt) REVERT: F 217 LYS cc_start: 0.7956 (ptpp) cc_final: 0.7452 (mttp) REVERT: F 422 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7564 (tm-30) REVERT: G 260 LYS cc_start: 0.8745 (tttt) cc_final: 0.8504 (tttp) REVERT: O 36 GLU cc_start: 0.6226 (tt0) cc_final: 0.6011 (tm-30) REVERT: O 37 LYS cc_start: 0.7106 (tptm) cc_final: 0.6747 (tppt) REVERT: O 42 VAL cc_start: 0.7131 (t) cc_final: 0.6802 (m) REVERT: O 134 LEU cc_start: 0.7728 (tp) cc_final: 0.7514 (mp) REVERT: O 186 MET cc_start: 0.6116 (ptp) cc_final: 0.5541 (pp-130) REVERT: D 145 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5765 (tp) REVERT: D 203 MET cc_start: 0.8477 (mtt) cc_final: 0.8181 (mtt) REVERT: D 259 ASP cc_start: 0.8221 (t0) cc_final: 0.7922 (t0) REVERT: D 479 GLU cc_start: 0.3841 (OUTLIER) cc_final: 0.3582 (mt-10) outliers start: 43 outliers final: 29 residues processed: 319 average time/residue: 1.4533 time to fit residues: 528.4089 Evaluate side-chains 304 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 269 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 2.9990 chunk 294 optimal weight: 0.0970 chunk 179 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 308 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 chunk 245 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN A 396 GLN B 70 ASN B 466 ASN B 503 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24300 Z= 0.147 Angle : 0.513 12.672 32875 Z= 0.254 Chirality : 0.042 0.229 3843 Planarity : 0.003 0.051 4244 Dihedral : 6.195 122.192 3505 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 1.53 % Allowed : 19.57 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 3105 helix: 1.17 (0.15), residues: 1337 sheet: -0.08 (0.24), residues: 489 loop : -0.38 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 476 PHE 0.013 0.001 PHE D 262 TYR 0.026 0.001 TYR F 371 ARG 0.008 0.000 ARG C 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 291 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8657 (ttm) cc_final: 0.8449 (ttt) REVERT: A 218 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7554 (tttt) REVERT: A 351 PHE cc_start: 0.7520 (m-80) cc_final: 0.7143 (t80) REVERT: A 362 ARG cc_start: 0.7606 (mtt180) cc_final: 0.6672 (mtt90) REVERT: A 466 ASN cc_start: 0.8077 (m-40) cc_final: 0.7760 (m110) REVERT: B 8 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6200 (mpm) REVERT: B 195 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: E 227 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: F 170 MET cc_start: 0.8819 (tpp) cc_final: 0.8551 (mmt) REVERT: F 171 GLU cc_start: 0.7382 (tp30) cc_final: 0.7113 (tp30) REVERT: F 422 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7446 (tm-30) REVERT: G 260 LYS cc_start: 0.8726 (tttt) cc_final: 0.8480 (tttp) REVERT: O 36 GLU cc_start: 0.6316 (tt0) cc_final: 0.6107 (tm-30) REVERT: O 37 LYS cc_start: 0.7052 (tptm) cc_final: 0.6740 (tppt) REVERT: O 42 VAL cc_start: 0.7143 (t) cc_final: 0.6811 (m) REVERT: O 134 LEU cc_start: 0.7814 (tp) cc_final: 0.7561 (mp) REVERT: O 186 MET cc_start: 0.6145 (ptp) cc_final: 0.5543 (pp-130) REVERT: D 145 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5845 (tp) REVERT: D 203 MET cc_start: 0.8473 (mtt) cc_final: 0.8182 (mtt) REVERT: D 259 ASP cc_start: 0.8206 (t0) cc_final: 0.7900 (t0) outliers start: 39 outliers final: 22 residues processed: 318 average time/residue: 1.4853 time to fit residues: 542.8152 Evaluate side-chains 296 residues out of total 2547 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 246 optimal weight: 0.0170 chunk 103 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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 B 432 GLN B 466 ASN B 503 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107097 restraints weight = 30800.014| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.10 r_work: 0.3163 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24300 Z= 0.188 Angle : 0.534 12.655 32875 Z= 0.264 Chirality : 0.043 0.244 3843 Planarity : 0.004 0.050 4244 Dihedral : 6.297 122.167 3505 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 1.34 % Allowed : 20.28 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3105 helix: 1.17 (0.15), residues: 1336 sheet: -0.06 (0.24), residues: 489 loop : -0.37 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 370 PHE 0.037 0.001 PHE C 464 TYR 0.024 0.001 TYR B 433 ARG 0.009 0.000 ARG C 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9524.70 seconds wall clock time: 169 minutes 35.52 seconds (10175.52 seconds total)