Starting phenix.real_space_refine on Thu Apr 11 18:10:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9p_34576/04_2024/8h9p_34576_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9p_34576/04_2024/8h9p_34576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9p_34576/04_2024/8h9p_34576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9p_34576/04_2024/8h9p_34576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9p_34576/04_2024/8h9p_34576_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9p_34576/04_2024/8h9p_34576_updated.pdb" } resolution = 3.02 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= 0.021 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 84 5.16 5 C 14744 2.51 5 N 4077 2.21 5 O 4495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" 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 GLU 440": "OE1" <-> "OE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 451": "OE1" <-> "OE2" Residue "F PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "O TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 151": "OE1" <-> "OE2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 172": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23418 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3287 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.21, per 1000 atoms: 0.52 Number of scatterers: 23418 At special positions: 0 Unit cell: (129.21, 123.37, 134.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 13 15.00 Mg 5 11.99 O 4495 8.00 N 4077 7.00 C 14744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.75 Conformation dependent library (CDL) restraints added in 5.0 seconds 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 22 sheets defined 40.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... 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 155 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.827A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 240 through 259 Proline residue: A 247 - end of helix removed outlier: 3.920A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.404A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (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 375 through 378 Processing helix chain 'A' and resid 381 through 403 removed outlier: 4.115A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 5.235A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.560A pdb=" N GLY A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 190 removed outlier: 4.334A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.633A 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 240 through 260 Proline residue: B 247 - end of helix removed outlier: 3.970A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 283 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: 4.080A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.127A 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 381 through 400 removed outlier: 4.376A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.851A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 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: 3.787A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 260 Proline residue: C 247 - end of helix removed outlier: 4.070A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.835A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 400 removed outlier: 4.195A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 458 through 475 removed outlier: 3.738A pdb=" N ILE C 461 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 468 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 229 through 248 removed outlier: 4.847A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 288 through 298 removed outlier: 4.712A pdb=" N ARG E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 323 through 331 removed outlier: 3.944A pdb=" N ALA E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS E 331 " --> pdb=" O THR E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 344 No H-bonds generated for 'chain 'E' and resid 341 through 344' Processing helix chain 'E' and resid 363 through 390 removed outlier: 7.505A pdb=" N SER E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLU E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 428 removed outlier: 5.089A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR E 428 " --> pdb=" O GLU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 Processing helix chain 'E' and resid 457 through 459 No H-bonds generated for 'chain 'E' and resid 457 through 459' Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 4.687A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 272 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: 4.648A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N HIS F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.871A pdb=" N LEU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 393 removed outlier: 4.813A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.054A 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 425 through 427 No H-bonds generated for 'chain 'F' and resid 425 through 427' Processing helix chain 'F' and resid 437 through 448 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 475 Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 193 through 206 Processing helix chain 'D' and resid 229 through 250 removed outlier: 4.917A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 274 Processing helix chain 'D' and resid 293 through 296 No H-bonds generated for 'chain 'D' and resid 293 through 296' Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 368 through 387 Processing helix chain 'D' and resid 404 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 476 Processing helix chain 'G' and resid 3 through 29 Processing helix chain 'G' and resid 224 through 269 Processing helix chain 'O' and resid 13 through 27 Processing helix chain 'O' and resid 32 through 46 Processing helix chain 'O' and resid 49 through 56 removed outlier: 4.232A pdb=" N LEU O 56 " --> pdb=" O ALA O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 removed outlier: 3.763A pdb=" N LYS O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.939A pdb=" N GLN O 99 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 139 Processing helix chain 'O' and resid 156 through 158 No H-bonds generated for 'chain 'O' and resid 156 through 158' Processing helix chain 'O' and resid 175 through 187 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.508A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.211A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 349 through 351 removed outlier: 7.063A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.690A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.439A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 35 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.257A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.884A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.786A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.534A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.277A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= L, first strand: chain 'C' and resid 229 through 234 removed outlier: 9.011A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.494A 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: 6.787A pdb=" N HIS C 263 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE C 202 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU C 265 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL C 204 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE C 266 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (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: 6.734A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE E 16 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.059A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 218 through 224 removed outlier: 6.654A pdb=" N SER E 184 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL E 221 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE E 186 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY E 223 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY E 188 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N VAL E 185 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU E 255 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA E 187 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE E 257 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 189 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP E 259 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU E 191 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER E 306 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU E 256 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 308 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE E 258 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 310 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY E 156 " --> pdb=" O ASP E 333 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR E 335 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE E 158 " --> pdb=" O THR E 335 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL E 337 " --> pdb=" O PHE E 158 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.694A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.666A 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: 4.229A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 334 through 337 removed outlier: 7.489A pdb=" N ILE F 155 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER F 309 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU F 157 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN F 311 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLY F 159 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE F 313 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA F 219 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY F 188 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL F 221 " --> pdb=" O GLY F 188 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.419A pdb=" N ASP D 25 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 19 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE D 64 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL D 52 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.064A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 154 through 156 removed outlier: 8.826A pdb=" N ILE D 155 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER D 309 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA D 219 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY D 188 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL D 221 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY D 190 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY D 223 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 147 through 150 935 hydrogen bonds defined for protein. 2613 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: 8.02 Time building geometry restraints manager: 10.30 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: 5294 1.33 - 1.45: 4409 1.45 - 1.57: 13866 1.57 - 1.69: 21 1.69 - 1.81: 161 Bond restraints: 23751 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 1.29e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.26e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.460 -0.123 1.10e-02 8.26e+03 1.25e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.00e-02 1.00e+04 7.87e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.286 0.088 1.00e-02 1.00e+04 7.71e+01 ... (remaining 23746 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.61: 644 106.61 - 114.40: 14343 114.40 - 122.19: 13350 122.19 - 129.98: 3735 129.98 - 137.78: 52 Bond angle restraints: 32124 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.98 17.89 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.43 17.44 1.00e+00 1.00e+00 3.04e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.84 14.03 1.00e+00 1.00e+00 1.97e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 123.16 13.67 1.00e+00 1.00e+00 1.87e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 123.40 13.43 1.00e+00 1.00e+00 1.80e+02 ... (remaining 32119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 14044 29.05 - 58.10: 473 58.10 - 87.16: 54 87.16 - 116.21: 5 116.21 - 145.26: 2 Dihedral angle restraints: 14578 sinusoidal: 5899 harmonic: 8679 Sorted by residual: dihedral pdb=" CD ARG C 373 " pdb=" NE ARG C 373 " pdb=" CZ ARG C 373 " pdb=" NH1 ARG C 373 " ideal model delta sinusoidal sigma weight residual 0.00 70.48 -70.48 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 154.74 145.26 1 2.00e+01 2.50e-03 4.37e+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 59.26 -119.25 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 14575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2823 0.050 - 0.100: 740 0.100 - 0.150: 172 0.150 - 0.200: 10 0.200 - 0.250: 3 Chirality restraints: 3748 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 1.56e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.42e+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 -2.46 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3745 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 373 " 1.023 9.50e-02 1.11e+02 4.58e-01 1.27e+02 pdb=" NE ARG C 373 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 373 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 373 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 373 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 277 " -0.274 9.50e-02 1.11e+02 1.23e-01 9.22e+00 pdb=" NE ARG D 277 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 277 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 277 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 277 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 322 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO E 323 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 323 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 323 " 0.025 5.00e-02 4.00e+02 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 209 2.56 - 3.15: 19536 3.15 - 3.73: 35919 3.73 - 4.32: 53728 4.32 - 4.90: 88577 Nonbonded interactions: 197969 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.976 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.982 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.983 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.144 2.170 ... (remaining 197964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 12 through 475) selection = (chain 'E' and (resid 12 through 160 or resid 162 through 312 or resid 330 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) selection = (chain 'F' and (resid 12 through 160 or resid 162 through 312 or resid 330 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 29.400 Check model and map are aligned: 0.340 Set scattering table: 0.230 Process input model: 64.810 Find NCS groups from input model: 1.780 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.006 0.147 23751 Z= 0.419 Angle : 0.793 17.889 32124 Z= 0.520 Chirality : 0.046 0.250 3748 Planarity : 0.008 0.458 4144 Dihedral : 14.266 145.261 9030 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -2.96 (0.13), residues: 3027 helix: -1.47 (0.12), residues: 1259 sheet: -2.12 (0.20), residues: 492 loop : -2.27 (0.15), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 476 PHE 0.017 0.001 PHE D 444 TYR 0.015 0.001 TYR C 446 ARG 0.004 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 420 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7744 (ttmt) REVERT: A 475 GLN cc_start: 0.6701 (mp10) cc_final: 0.6434 (mp10) REVERT: B 89 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7625 (mtpt) REVERT: B 226 MET cc_start: 0.8227 (mmm) cc_final: 0.7848 (tpt) REVERT: B 396 GLN cc_start: 0.8196 (mt0) cc_final: 0.7933 (mm-40) REVERT: B 418 LEU cc_start: 0.8081 (mp) cc_final: 0.7725 (tt) REVERT: B 477 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7187 (tm-30) REVERT: E 347 ILE cc_start: 0.9261 (mm) cc_final: 0.8886 (mm) REVERT: D 62 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7677 (ttm-80) REVERT: D 128 GLU cc_start: 0.8248 (tt0) cc_final: 0.7946 (mt-10) REVERT: D 339 SER cc_start: 0.8174 (t) cc_final: 0.7762 (p) REVERT: D 433 LYS cc_start: 0.6842 (mmtm) cc_final: 0.6288 (mptt) REVERT: D 445 GLN cc_start: 0.6212 (tm-30) cc_final: 0.5883 (pt0) REVERT: D 455 LEU cc_start: 0.6748 (mm) cc_final: 0.6503 (mm) REVERT: D 460 PHE cc_start: 0.6978 (m-10) cc_final: 0.6777 (m-10) REVERT: D 462 MET cc_start: 0.8140 (tpt) cc_final: 0.7575 (tpp) REVERT: D 467 GLU cc_start: 0.7027 (tt0) cc_final: 0.6804 (mp0) REVERT: G 229 MET cc_start: 0.7549 (ttp) cc_final: 0.7166 (ttm) REVERT: O 33 GLU cc_start: 0.6064 (mp0) cc_final: 0.4520 (tp30) outliers start: 3 outliers final: 1 residues processed: 421 average time/residue: 0.4290 time to fit residues: 267.8346 Evaluate side-chains 289 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 385 GLN A 396 GLN A 503 ASN B 65 ASN B 471 HIS B 475 GLN C 78 ASN C 208 GLN C 385 GLN C 471 HIS C 475 GLN E 370 HIS F 133 GLN F 174 ASN F 197 ASN F 311 GLN F 331 HIS D 260 ASN D 285 GLN D 378 GLN D 382 GLN D 419 GLN O 10 GLN O 92 ASN O 99 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23751 Z= 0.269 Angle : 0.577 13.615 32124 Z= 0.290 Chirality : 0.045 0.147 3748 Planarity : 0.004 0.041 4144 Dihedral : 7.842 128.427 3428 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 1.17 % Allowed : 9.61 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -1.55 (0.14), residues: 3027 helix: -0.19 (0.14), residues: 1252 sheet: -1.62 (0.21), residues: 487 loop : -1.51 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 476 PHE 0.019 0.001 PHE D 444 TYR 0.024 0.002 TYR E 384 ARG 0.005 0.000 ARG D 415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 315 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7903 (ttp-110) REVERT: A 460 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7711 (ttmt) REVERT: A 475 GLN cc_start: 0.6947 (mp10) cc_final: 0.6664 (mp10) REVERT: B 89 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7781 (mtpt) REVERT: B 226 MET cc_start: 0.8255 (mmm) cc_final: 0.7924 (tpt) REVERT: B 418 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 477 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7152 (tm-30) REVERT: E 347 ILE cc_start: 0.9252 (mm) cc_final: 0.8886 (mm) REVERT: D 62 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7620 (ttm-80) REVERT: D 128 GLU cc_start: 0.8174 (tt0) cc_final: 0.7943 (mt-10) REVERT: D 297 GLU cc_start: 0.7744 (tp30) cc_final: 0.7512 (tp30) REVERT: D 339 SER cc_start: 0.8189 (t) cc_final: 0.7786 (p) REVERT: D 433 LYS cc_start: 0.6872 (mmtm) cc_final: 0.6304 (mptt) REVERT: D 445 GLN cc_start: 0.6172 (tm-30) cc_final: 0.5843 (pt0) REVERT: D 462 MET cc_start: 0.8117 (tpt) cc_final: 0.7495 (tpp) REVERT: D 467 GLU cc_start: 0.7009 (tt0) cc_final: 0.6788 (mp0) REVERT: O 33 GLU cc_start: 0.6112 (mp0) cc_final: 0.4627 (tp30) outliers start: 29 outliers final: 14 residues processed: 331 average time/residue: 0.4055 time to fit residues: 206.0924 Evaluate side-chains 289 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain O residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 228 optimal weight: 0.3980 chunk 186 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 274 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN B 475 GLN E 174 ASN E 210 ASN F 174 ASN F 175 ASN D 296 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23751 Z= 0.175 Angle : 0.527 11.005 32124 Z= 0.264 Chirality : 0.043 0.161 3748 Planarity : 0.004 0.041 4144 Dihedral : 7.201 112.339 3428 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.44 % Favored : 97.49 % Rotamer: Outliers : 1.53 % Allowed : 11.34 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.83 (0.15), residues: 3027 helix: 0.38 (0.15), residues: 1260 sheet: -1.30 (0.22), residues: 480 loop : -1.08 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 476 PHE 0.013 0.001 PHE A 504 TYR 0.026 0.001 TYR E 384 ARG 0.005 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 318 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7728 (ttmt) REVERT: A 475 GLN cc_start: 0.7022 (mp10) cc_final: 0.6753 (mp10) REVERT: B 89 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7738 (mtpt) REVERT: B 226 MET cc_start: 0.8267 (mmm) cc_final: 0.8035 (tpt) REVERT: B 418 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7689 (tt) REVERT: B 477 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7169 (tm-30) REVERT: C 45 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7895 (mmm160) REVERT: E 347 ILE cc_start: 0.9220 (mm) cc_final: 0.8860 (mm) REVERT: E 427 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7827 (t80) REVERT: D 62 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7624 (ttm-80) REVERT: D 101 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8553 (mt) REVERT: D 263 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.7868 (mpt180) REVERT: D 433 LYS cc_start: 0.6870 (mmtm) cc_final: 0.6330 (mptt) REVERT: D 445 GLN cc_start: 0.6087 (tm-30) cc_final: 0.5826 (pt0) REVERT: D 462 MET cc_start: 0.8126 (tpt) cc_final: 0.7463 (tpp) REVERT: O 33 GLU cc_start: 0.6075 (mp0) cc_final: 0.4639 (tp30) REVERT: O 91 GLU cc_start: 0.6072 (pt0) cc_final: 0.5652 (mt-10) outliers start: 38 outliers final: 22 residues processed: 339 average time/residue: 0.3738 time to fit residues: 195.8278 Evaluate side-chains 308 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 283 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 184 optimal weight: 0.6980 chunk 275 optimal weight: 0.1980 chunk 291 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 274 GLN C 42 HIS E 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23751 Z= 0.168 Angle : 0.509 9.740 32124 Z= 0.255 Chirality : 0.043 0.162 3748 Planarity : 0.003 0.039 4144 Dihedral : 6.683 104.421 3428 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.46 % Rotamer: Outliers : 1.93 % Allowed : 12.31 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.41 (0.15), residues: 3027 helix: 0.69 (0.15), residues: 1260 sheet: -1.07 (0.23), residues: 477 loop : -0.82 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 476 PHE 0.012 0.001 PHE A 504 TYR 0.027 0.001 TYR E 384 ARG 0.005 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 311 time to evaluate : 3.182 Fit side-chains revert: symmetry clash REVERT: A 460 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7752 (ttmt) REVERT: A 475 GLN cc_start: 0.7006 (mp10) cc_final: 0.6754 (mp10) REVERT: B 89 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7719 (mtmt) REVERT: B 415 GLN cc_start: 0.7519 (mt0) cc_final: 0.6956 (mm-40) REVERT: B 418 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7714 (tt) REVERT: B 477 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7197 (tm-30) REVERT: C 397 TYR cc_start: 0.8160 (t80) cc_final: 0.7938 (t80) REVERT: E 347 ILE cc_start: 0.9220 (mm) cc_final: 0.8861 (mm) REVERT: E 427 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7834 (t80) REVERT: E 458 GLN cc_start: 0.7814 (tp40) cc_final: 0.7223 (tp40) REVERT: D 62 ARG cc_start: 0.7913 (ttm170) cc_final: 0.7639 (ttm-80) REVERT: D 101 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8642 (pt) REVERT: D 260 ASN cc_start: 0.7194 (m-40) cc_final: 0.6903 (m-40) REVERT: D 433 LYS cc_start: 0.6888 (mmtm) cc_final: 0.6353 (mptt) REVERT: D 445 GLN cc_start: 0.6056 (tm-30) cc_final: 0.5806 (pt0) REVERT: D 462 MET cc_start: 0.8079 (tpt) cc_final: 0.7420 (tpp) REVERT: O 33 GLU cc_start: 0.6031 (mp0) cc_final: 0.4664 (tp30) REVERT: O 91 GLU cc_start: 0.5964 (pt0) cc_final: 0.5730 (mt-10) outliers start: 48 outliers final: 25 residues processed: 339 average time/residue: 0.3923 time to fit residues: 207.8058 Evaluate side-chains 318 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 217 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN C 42 HIS E 174 ASN F 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23751 Z= 0.365 Angle : 0.588 9.009 32124 Z= 0.296 Chirality : 0.046 0.214 3748 Planarity : 0.004 0.038 4144 Dihedral : 6.933 108.042 3428 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 2.53 % Allowed : 13.15 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.47 (0.15), residues: 3027 helix: 0.60 (0.15), residues: 1261 sheet: -1.13 (0.22), residues: 499 loop : -0.78 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 476 PHE 0.014 0.001 PHE D 158 TYR 0.017 0.002 TYR A 256 ARG 0.009 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 293 time to evaluate : 2.609 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6922 (tm-30) REVERT: A 460 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7831 (ttmt) REVERT: A 475 GLN cc_start: 0.7153 (mp10) cc_final: 0.6850 (mp10) REVERT: B 89 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7746 (mtmt) REVERT: B 415 GLN cc_start: 0.7569 (mt0) cc_final: 0.7027 (mm-40) REVERT: B 418 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 477 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7164 (tm-30) REVERT: E 347 ILE cc_start: 0.9271 (mm) cc_final: 0.8924 (mm) REVERT: E 427 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7854 (t80) REVERT: D 62 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7656 (ttm-80) REVERT: D 414 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.5734 (mt0) REVERT: D 433 LYS cc_start: 0.6965 (mmtm) cc_final: 0.6378 (mptt) REVERT: D 445 GLN cc_start: 0.6126 (tm-30) cc_final: 0.5809 (pt0) REVERT: D 462 MET cc_start: 0.8164 (tpt) cc_final: 0.7486 (tpp) REVERT: O 33 GLU cc_start: 0.6112 (mp0) cc_final: 0.4653 (tp30) REVERT: O 91 GLU cc_start: 0.5972 (pt0) cc_final: 0.5731 (mt-10) outliers start: 63 outliers final: 43 residues processed: 333 average time/residue: 0.3715 time to fit residues: 191.2177 Evaluate side-chains 326 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 280 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN E 174 ASN D 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23751 Z= 0.248 Angle : 0.546 8.852 32124 Z= 0.273 Chirality : 0.044 0.178 3748 Planarity : 0.004 0.036 4144 Dihedral : 6.734 103.955 3428 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 2.65 % Allowed : 14.00 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.29 (0.15), residues: 3027 helix: 0.73 (0.15), residues: 1259 sheet: -0.97 (0.23), residues: 475 loop : -0.70 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 476 PHE 0.013 0.001 PHE D 444 TYR 0.017 0.001 TYR B 397 ARG 0.007 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 295 time to evaluate : 2.774 Fit side-chains revert: symmetry clash REVERT: A 460 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7839 (ttmt) REVERT: A 475 GLN cc_start: 0.7152 (mp10) cc_final: 0.6873 (mp10) REVERT: B 89 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7729 (mtmt) REVERT: B 418 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 477 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7189 (tm-30) REVERT: C 420 ARG cc_start: 0.6641 (tpp80) cc_final: 0.6280 (tpp-160) REVERT: E 347 ILE cc_start: 0.9233 (mm) cc_final: 0.8877 (mm) REVERT: E 427 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7842 (t80) REVERT: F 70 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: D 62 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7640 (ttm-80) REVERT: D 414 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5702 (mt0) REVERT: D 433 LYS cc_start: 0.6969 (mmtm) cc_final: 0.6425 (mptt) REVERT: D 445 GLN cc_start: 0.6102 (tm-30) cc_final: 0.5818 (pt0) REVERT: D 462 MET cc_start: 0.8147 (tpt) cc_final: 0.7479 (tpp) REVERT: G 23 MET cc_start: 0.6442 (ttm) cc_final: 0.6187 (ttm) REVERT: O 33 GLU cc_start: 0.6111 (mp0) cc_final: 0.4641 (tp30) outliers start: 66 outliers final: 40 residues processed: 340 average time/residue: 0.3789 time to fit residues: 199.9501 Evaluate side-chains 323 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 279 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 166 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 GLN E 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23751 Z= 0.254 Angle : 0.547 8.605 32124 Z= 0.273 Chirality : 0.044 0.165 3748 Planarity : 0.004 0.035 4144 Dihedral : 6.588 97.275 3428 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 2.33 % Allowed : 14.52 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.23 (0.15), residues: 3027 helix: 0.77 (0.15), residues: 1265 sheet: -0.91 (0.23), residues: 475 loop : -0.66 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 476 PHE 0.012 0.001 PHE D 444 TYR 0.018 0.001 TYR B 397 ARG 0.004 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 294 time to evaluate : 2.870 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6877 (tm-30) REVERT: A 460 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7861 (ttmt) REVERT: A 475 GLN cc_start: 0.7154 (mp10) cc_final: 0.6864 (mp10) REVERT: B 89 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7767 (mtmt) REVERT: B 418 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7688 (tt) REVERT: B 477 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7176 (tm-30) REVERT: E 347 ILE cc_start: 0.9239 (mm) cc_final: 0.8888 (mm) REVERT: E 427 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7854 (t80) REVERT: F 70 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: D 62 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7619 (ttm-80) REVERT: D 127 MET cc_start: 0.8085 (mmm) cc_final: 0.7738 (mmm) REVERT: D 205 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 347 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6783 (mp) REVERT: D 414 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5708 (mt0) REVERT: D 433 LYS cc_start: 0.6964 (mmtm) cc_final: 0.6437 (mptt) REVERT: D 445 GLN cc_start: 0.6075 (tm-30) cc_final: 0.5780 (pt0) REVERT: D 462 MET cc_start: 0.8113 (tpt) cc_final: 0.7487 (tpp) REVERT: G 23 MET cc_start: 0.6378 (ttm) cc_final: 0.6120 (ttm) REVERT: O 33 GLU cc_start: 0.6115 (mp0) cc_final: 0.4594 (tp30) outliers start: 58 outliers final: 44 residues processed: 333 average time/residue: 0.3712 time to fit residues: 193.3572 Evaluate side-chains 328 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 278 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 228 optimal weight: 0.0970 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 503 ASN B 432 GLN B 475 GLN F 115 GLN D 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23751 Z= 0.155 Angle : 0.510 8.482 32124 Z= 0.255 Chirality : 0.043 0.167 3748 Planarity : 0.003 0.039 4144 Dihedral : 6.106 77.880 3428 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 2.25 % Allowed : 14.88 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.00 (0.16), residues: 3027 helix: 0.95 (0.15), residues: 1269 sheet: -0.89 (0.23), residues: 494 loop : -0.48 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 476 PHE 0.012 0.001 PHE D 444 TYR 0.019 0.001 TYR B 397 ARG 0.003 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 314 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6894 (tm-30) REVERT: A 475 GLN cc_start: 0.7052 (mp10) cc_final: 0.6806 (mp10) REVERT: B 89 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7714 (mtmt) REVERT: B 418 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7696 (tt) REVERT: B 477 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7215 (tm-30) REVERT: E 347 ILE cc_start: 0.9195 (mm) cc_final: 0.8841 (mm) REVERT: E 384 TYR cc_start: 0.8212 (t80) cc_final: 0.7997 (t80) REVERT: E 427 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7860 (t80) REVERT: F 70 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: F 398 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: D 62 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7594 (ttm-80) REVERT: D 347 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6750 (mp) REVERT: D 414 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5668 (mt0) REVERT: D 433 LYS cc_start: 0.6959 (mmtm) cc_final: 0.6503 (mptt) REVERT: D 445 GLN cc_start: 0.5989 (tm-30) cc_final: 0.5761 (pt0) REVERT: D 462 MET cc_start: 0.8143 (tpt) cc_final: 0.7483 (tpp) REVERT: G 23 MET cc_start: 0.6264 (ttm) cc_final: 0.6044 (ttm) REVERT: O 33 GLU cc_start: 0.6088 (mp0) cc_final: 0.4611 (tp30) REVERT: O 159 LEU cc_start: 0.7687 (pp) cc_final: 0.6988 (mm) outliers start: 56 outliers final: 38 residues processed: 351 average time/residue: 0.3751 time to fit residues: 206.0896 Evaluate side-chains 340 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 296 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 0.0870 chunk 278 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 271 optimal weight: 6.9990 chunk 163 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 270 optimal weight: 0.7980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23751 Z= 0.157 Angle : 0.516 9.792 32124 Z= 0.256 Chirality : 0.043 0.164 3748 Planarity : 0.003 0.043 4144 Dihedral : 5.961 69.287 3428 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 1.97 % Allowed : 15.33 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.11 (0.16), residues: 3027 helix: 1.03 (0.15), residues: 1270 sheet: -0.82 (0.23), residues: 494 loop : -0.42 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS B 476 PHE 0.012 0.001 PHE E 262 TYR 0.019 0.001 TYR B 397 ARG 0.009 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 303 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 475 GLN cc_start: 0.7053 (mp10) cc_final: 0.6817 (mp10) REVERT: B 89 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7694 (mtmt) REVERT: B 418 LEU cc_start: 0.8079 (mp) cc_final: 0.7734 (tt) REVERT: B 475 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7421 (mm-40) REVERT: E 347 ILE cc_start: 0.9195 (mm) cc_final: 0.8861 (mm) REVERT: E 427 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7856 (t80) REVERT: E 462 MET cc_start: 0.8659 (mmt) cc_final: 0.7660 (mmm) REVERT: F 70 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: F 398 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: D 62 ARG cc_start: 0.7886 (ttm170) cc_final: 0.7596 (ttm-80) REVERT: D 347 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6744 (mp) REVERT: D 414 GLN cc_start: 0.6258 (OUTLIER) cc_final: 0.5654 (mt0) REVERT: D 433 LYS cc_start: 0.6951 (mmtm) cc_final: 0.6483 (mptt) REVERT: D 445 GLN cc_start: 0.5969 (tm-30) cc_final: 0.5751 (pt0) REVERT: D 462 MET cc_start: 0.8148 (tpt) cc_final: 0.7484 (tpp) REVERT: G 23 MET cc_start: 0.6221 (ttm) cc_final: 0.6006 (ttm) REVERT: O 33 GLU cc_start: 0.6085 (mp0) cc_final: 0.4612 (tp30) REVERT: O 159 LEU cc_start: 0.7692 (pp) cc_final: 0.7008 (mm) outliers start: 49 outliers final: 35 residues processed: 335 average time/residue: 0.3805 time to fit residues: 198.8055 Evaluate side-chains 329 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 288 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 0.8980 chunk 286 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 239 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 GLN C 385 GLN E 311 GLN D 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 23751 Z= 0.475 Angle : 0.647 8.906 32124 Z= 0.325 Chirality : 0.048 0.174 3748 Planarity : 0.004 0.042 4144 Dihedral : 6.580 83.760 3428 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 1.89 % Allowed : 15.65 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.24 (0.15), residues: 3027 helix: 0.68 (0.15), residues: 1269 sheet: -0.93 (0.22), residues: 496 loop : -0.56 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 476 PHE 0.020 0.002 PHE D 158 TYR 0.021 0.002 TYR B 397 ARG 0.008 0.000 ARG A 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 280 time to evaluate : 2.989 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 460 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7804 (ttmt) REVERT: A 475 GLN cc_start: 0.7246 (mp10) cc_final: 0.6950 (mp10) REVERT: B 89 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7783 (mtmt) REVERT: B 418 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7710 (tt) REVERT: E 347 ILE cc_start: 0.9297 (mm) cc_final: 0.8959 (mm) REVERT: E 427 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7868 (t80) REVERT: F 70 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: F 398 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: D 62 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7644 (ttm-80) REVERT: D 347 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6696 (mp) REVERT: D 414 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.5751 (mt0) REVERT: D 417 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7235 (pp) REVERT: D 433 LYS cc_start: 0.7073 (mmtm) cc_final: 0.6561 (mptt) REVERT: D 445 GLN cc_start: 0.6021 (tm-30) cc_final: 0.5741 (pt0) REVERT: D 462 MET cc_start: 0.8142 (tpt) cc_final: 0.7484 (tpp) REVERT: G 23 MET cc_start: 0.6440 (ttm) cc_final: 0.6166 (ttm) REVERT: O 33 GLU cc_start: 0.6141 (mp0) cc_final: 0.4556 (tp30) outliers start: 47 outliers final: 37 residues processed: 312 average time/residue: 0.3883 time to fit residues: 186.6298 Evaluate side-chains 317 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 239 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 GLN C 385 GLN E 311 GLN F 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101008 restraints weight = 33926.932| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.14 r_work: 0.3163 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23751 Z= 0.173 Angle : 0.546 8.270 32124 Z= 0.271 Chirality : 0.043 0.174 3748 Planarity : 0.003 0.037 4144 Dihedral : 6.126 75.020 3428 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 1.81 % Allowed : 15.97 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 (0.16), residues: 3027 helix: 0.92 (0.15), residues: 1269 sheet: -0.81 (0.23), residues: 480 loop : -0.46 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 476 PHE 0.016 0.001 PHE A 464 TYR 0.021 0.001 TYR B 397 ARG 0.008 0.000 ARG A 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5680.85 seconds wall clock time: 104 minutes 52.37 seconds (6292.37 seconds total)