Starting phenix.real_space_refine on Sat Aug 10 10:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/08_2024/8x7u_38111.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/08_2024/8x7u_38111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/08_2024/8x7u_38111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/08_2024/8x7u_38111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/08_2024/8x7u_38111.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/08_2024/8x7u_38111.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.024 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 12 5.49 5 Mg 3 5.21 5 S 83 5.16 5 C 18300 2.51 5 N 5164 2.21 5 O 5270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D ASP 478": "OD1" <-> "OD2" Residue "D ASP 545": "OD1" <-> "OD2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 478": "OD1" <-> "OD2" Residue "C TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 503": "OD1" <-> "OD2" Residue "C ASP 545": "OD1" <-> "OD2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "E ASP 45": "OD1" <-> "OD2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 401": "NH1" <-> "NH2" Residue "E PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 475": "OE1" <-> "OE2" Residue "E GLU 494": "OE1" <-> "OE2" Residue "E ASP 580": "OD1" <-> "OD2" Residue "E ASP 604": "OD1" <-> "OD2" Residue "E GLU 621": "OE1" <-> "OE2" Residue "E TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 210": "OD1" <-> "OD2" Residue "F ASP 211": "OD1" <-> "OD2" Residue "F GLU 272": "OE1" <-> "OE2" Residue "F ASP 285": "OD1" <-> "OD2" Residue "F ARG 401": "NH1" <-> "NH2" Residue "F ASP 402": "OD1" <-> "OD2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F ASP 454": "OD1" <-> "OD2" Residue "F ASP 471": "OD1" <-> "OD2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "F GLU 475": "OE1" <-> "OE2" Residue "F ASP 478": "OD1" <-> "OD2" Residue "F TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "F GLU 574": "OE1" <-> "OE2" Residue "F GLU 589": "OE1" <-> "OE2" Residue "F TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 28832 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 4922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4922 Classifications: {'peptide': 654} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 30, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 170 Chain: "C" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4893 Classifications: {'peptide': 654} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 30, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 4817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4817 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 29, 'TRANS': 612} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 19, 'ASN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 168 Chain: "E" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4881 Classifications: {'peptide': 654} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 30, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 191 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4343 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 28, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 214 Chain: "F" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 4830 Classifications: {'peptide': 653} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 30, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 247 Chain: "D" 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: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 16.41, per 1000 atoms: 0.57 Number of scatterers: 28832 At special positions: 0 Unit cell: (139.8, 138.868, 179.876, 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 83 16.00 P 12 15.00 Mg 3 11.99 O 5270 8.00 N 5164 7.00 C 18300 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: 11.17 Conformation dependent library (CDL) restraints added in 5.3 seconds 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7286 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 44 sheets defined 42.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.567A pdb=" N VAL D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 53 through 63 removed outlier: 3.599A pdb=" N ALA D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.953A pdb=" N ALA D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.573A pdb=" N ILE D 113 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'D' and resid 294 through 306 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.648A pdb=" N VAL D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 Processing helix chain 'D' and resid 401 through 404 removed outlier: 3.662A pdb=" N SER D 404 " --> pdb=" O ARG D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.735A pdb=" N GLU D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 422 removed outlier: 3.749A pdb=" N GLY D 421 " --> pdb=" O SER D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 removed outlier: 3.634A pdb=" N LEU D 460 " --> pdb=" O PRO D 456 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 461 " --> pdb=" O PRO D 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 461' Processing helix chain 'D' and resid 474 through 491 Processing helix chain 'D' and resid 501 through 516 Processing helix chain 'D' and resid 521 through 536 Processing helix chain 'D' and resid 553 through 571 removed outlier: 3.720A pdb=" N ARG D 571 " --> pdb=" O HIS D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 596 Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 640 through 651 Processing helix chain 'D' and resid 654 through 669 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.555A pdb=" N ALA C 8 " --> pdb=" O GLU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.986A pdb=" N LEU C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.505A pdb=" N PHE C 52 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.648A pdb=" N LEU C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 78 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.583A pdb=" N ILE C 113 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.590A pdb=" N GLU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.624A pdb=" N GLN C 268 " --> pdb=" O PRO C 264 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.894A pdb=" N VAL C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 344 " --> pdb=" O ARG C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.035A pdb=" N GLU C 411 " --> pdb=" O HIS C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.717A pdb=" N GLN C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 461 removed outlier: 3.512A pdb=" N LEU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 461 " --> pdb=" O PRO C 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 456 through 461' Processing helix chain 'C' and resid 474 through 491 Processing helix chain 'C' and resid 492 through 497 removed outlier: 3.856A pdb=" N VAL C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 516 removed outlier: 3.922A pdb=" N LYS C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 538 Processing helix chain 'C' and resid 553 through 571 removed outlier: 3.520A pdb=" N LEU C 557 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C 571 " --> pdb=" O HIS C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 596 Processing helix chain 'C' and resid 603 through 608 removed outlier: 4.116A pdb=" N ILE C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 622 Processing helix chain 'C' and resid 640 through 645 removed outlier: 3.708A pdb=" N ILE C 644 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 650 removed outlier: 3.541A pdb=" N ALA C 650 " --> pdb=" O ALA C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 668 removed outlier: 3.672A pdb=" N SER C 667 " --> pdb=" O ASN C 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.640A pdb=" N ASP B 32 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.546A pdb=" N LEU B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 removed outlier: 3.904A pdb=" N ALA B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.722A pdb=" N HIS B 112 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 113 " --> pdb=" O SER B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 113' Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.658A pdb=" N GLY B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.671A pdb=" N GLN B 268 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 294 through 306 Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.800A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.544A pdb=" N ALA B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 410 removed outlier: 3.691A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 removed outlier: 3.686A pdb=" N GLN B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 474 through 491 Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.532A pdb=" N LYS B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 536 removed outlier: 3.579A pdb=" N ARG B 536 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 571 Processing helix chain 'B' and resid 577 through 595 removed outlier: 3.527A pdb=" N THR B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 3.611A pdb=" N ILE B 620 " --> pdb=" O LYS B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 650 removed outlier: 3.695A pdb=" N ILE B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.692A pdb=" N LEU B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.864A pdb=" N ASP E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 53 removed outlier: 3.535A pdb=" N SER E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE E 52 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 63 removed outlier: 3.611A pdb=" N LEU E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 81 removed outlier: 3.595A pdb=" N ALA E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 278 through 287 Processing helix chain 'E' and resid 294 through 306 Processing helix chain 'E' and resid 334 through 346 removed outlier: 3.659A pdb=" N ALA E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 344 " --> pdb=" O ARG E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 Processing helix chain 'E' and resid 394 through 398 removed outlier: 3.785A pdb=" N MET E 398 " --> pdb=" O PHE E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 405 removed outlier: 4.426A pdb=" N ALA E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 412 removed outlier: 3.697A pdb=" N LEU E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.577A pdb=" N LEU E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 461 " --> pdb=" O PRO E 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 456 through 461' Processing helix chain 'E' and resid 474 through 491 removed outlier: 3.640A pdb=" N SER E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 497 removed outlier: 4.025A pdb=" N VAL E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 513 removed outlier: 3.813A pdb=" N LYS E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 539 through 543 removed outlier: 3.741A pdb=" N ASP E 543 " --> pdb=" O ARG E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 571 removed outlier: 3.530A pdb=" N ALA E 559 " --> pdb=" O ARG E 555 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 568 " --> pdb=" O SER E 564 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 571 " --> pdb=" O HIS E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 596 removed outlier: 3.615A pdb=" N ALA E 581 " --> pdb=" O THR E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 622 Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.727A pdb=" N GLU E 645 " --> pdb=" O GLU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 669 removed outlier: 3.517A pdb=" N LYS E 660 " --> pdb=" O ALA E 656 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP E 668 " --> pdb=" O GLU E 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.880A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.722A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 81 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.567A pdb=" N ILE A 113 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 278 through 287 removed outlier: 4.339A pdb=" N VAL A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.609A pdb=" N ALA A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.972A pdb=" N HIS A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.921A pdb=" N GLY A 421 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 removed outlier: 3.818A pdb=" N GLN A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 removed outlier: 3.654A pdb=" N SER A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 491 Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.722A pdb=" N VAL A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 515 removed outlier: 3.563A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 3.735A pdb=" N TYR A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 571 removed outlier: 3.548A pdb=" N ALA A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.513A pdb=" N ILE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 28 through 36 removed outlier: 4.030A pdb=" N ASP F 32 " --> pdb=" O ASN F 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 3.576A pdb=" N SER F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 removed outlier: 3.555A pdb=" N ALA F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 81 removed outlier: 3.581A pdb=" N ALA F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.637A pdb=" N ILE F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 263 through 276 removed outlier: 3.529A pdb=" N GLN F 268 " --> pdb=" O PRO F 264 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 287 removed outlier: 3.660A pdb=" N VAL F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 306 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 337 through 346 removed outlier: 3.951A pdb=" N ALA F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN F 344 " --> pdb=" O ARG F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 Processing helix chain 'F' and resid 399 through 410 removed outlier: 4.185A pdb=" N ALA F 405 " --> pdb=" O ARG F 401 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HIS F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 456 through 463 removed outlier: 3.791A pdb=" N LEU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER F 461 " --> pdb=" O PRO F 457 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG F 462 " --> pdb=" O THR F 458 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE F 463 " --> pdb=" O LEU F 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 456 through 463' Processing helix chain 'F' and resid 474 through 491 removed outlier: 3.774A pdb=" N ASP F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 485 " --> pdb=" O ILE F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 497 removed outlier: 3.984A pdb=" N VAL F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 515 removed outlier: 3.698A pdb=" N LYS F 507 " --> pdb=" O ASP F 503 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR F 508 " --> pdb=" O LEU F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 Processing helix chain 'F' and resid 553 through 571 removed outlier: 3.579A pdb=" N ALA F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 571 " --> pdb=" O HIS F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 596 removed outlier: 3.709A pdb=" N ALA F 596 " --> pdb=" O MET F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 620 removed outlier: 3.918A pdb=" N ILE F 620 " --> pdb=" O LYS F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 650 removed outlier: 3.500A pdb=" N ILE F 644 " --> pdb=" O GLU F 640 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 645 " --> pdb=" O GLU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 667 removed outlier: 3.785A pdb=" N LYS F 660 " --> pdb=" O ALA F 656 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 662 " --> pdb=" O ILE F 658 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 665 " --> pdb=" O LEU F 661 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.312A pdb=" N LEU D 42 " --> pdb=" O ARG D 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 103 through 104 removed outlier: 7.079A pdb=" N LEU D 103 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N ILE D 122 " --> pdb=" O LEU D 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 119 through 126 current: chain 'D' and resid 148 through 150 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 148 through 150 current: chain 'D' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 203 through 208 current: chain 'D' and resid 242 through 249 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 242 through 249 current: chain 'D' and resid 375 through 378 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 388 through 390 removed outlier: 5.990A pdb=" N VAL D 325 " --> pdb=" O ALA D 434 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU D 326 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU D 469 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL D 328 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.704A pdb=" N THR D 352 " --> pdb=" O ASP D 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 414 through 417 Processing sheet with id=AA6, first strand: chain 'D' and resid 519 through 520 removed outlier: 6.995A pdb=" N VAL D 519 " --> pdb=" O VAL D 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.118A pdb=" N LEU C 42 " --> pdb=" O ARG C 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 104 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 116 through 126 current: chain 'C' and resid 147 through 150 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 147 through 150 current: chain 'C' and resid 203 through 209 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 203 through 209 current: chain 'C' and resid 245 through 249 Processing sheet with id=AA9, first strand: chain 'C' and resid 433 through 434 removed outlier: 6.026A pdb=" N VAL C 325 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.618A pdb=" N THR C 352 " --> pdb=" O ASP C 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 365 through 368 Processing sheet with id=AB3, first strand: chain 'C' and resid 414 through 419 removed outlier: 3.787A pdb=" N ALA C 424 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 519 through 520 removed outlier: 6.928A pdb=" N VAL C 519 " --> pdb=" O VAL C 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 44 removed outlier: 3.664A pdb=" N LEU B 42 " --> pdb=" O HIS B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 103 through 104 removed outlier: 6.937A pdb=" N LEU B 103 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N ILE B 122 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP B 220 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B 225 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 242 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LYS B 243 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 205 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 247 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER B 185 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 126 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 187 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 132 through 135 removed outlier: 7.101A pdb=" N ARG B 179 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AB9, first strand: chain 'B' and resid 388 through 390 removed outlier: 7.309A pdb=" N GLY B 388 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE B 433 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 390 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL B 325 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 326 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 469 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 328 " --> pdb=" O LEU B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 353 removed outlier: 6.806A pdb=" N THR B 352 " --> pdb=" O ASP B 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 365 through 368 Processing sheet with id=AC3, first strand: chain 'B' and resid 414 through 419 Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 removed outlier: 7.092A pdb=" N VAL B 519 " --> pdb=" O VAL B 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 43 through 45 removed outlier: 3.526A pdb=" N TYR E 97 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 103 through 104 removed outlier: 6.921A pdb=" N LEU E 103 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ILE E 122 " --> pdb=" O LEU E 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 119 through 126 current: chain 'E' and resid 148 through 149 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 148 through 149 current: chain 'E' and resid 203 through 209 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 203 through 209 current: chain 'E' and resid 243 through 249 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 433 through 436 removed outlier: 6.016A pdb=" N VAL E 325 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA E 436 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 327 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 326 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU E 469 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL E 328 " --> pdb=" O LEU E 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 352 through 353 removed outlier: 6.744A pdb=" N THR E 352 " --> pdb=" O ASP E 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 365 through 368 Processing sheet with id=AD1, first strand: chain 'E' and resid 388 through 389 removed outlier: 7.301A pdb=" N GLY E 388 " --> pdb=" O THR E 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 414 through 417 Processing sheet with id=AD3, first strand: chain 'E' and resid 519 through 520 removed outlier: 6.934A pdb=" N VAL E 519 " --> pdb=" O VAL E 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 671 through 672 Processing sheet with id=AD5, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AD6, first strand: chain 'A' and resid 130 through 135 removed outlier: 7.327A pdb=" N ARG A 179 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LEU A 245 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP A 205 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL A 247 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 207 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS A 249 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 225 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A 187 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 126 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER A 185 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AD8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.943A pdb=" N ILE A 350 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 391 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY A 388 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 433 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 390 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA A 435 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 392 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 325 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 364 through 368 removed outlier: 3.844A pdb=" N ALA A 365 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 367 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 414 through 417 Processing sheet with id=AE2, first strand: chain 'F' and resid 102 through 104 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 102 through 104 current: chain 'F' and resid 203 through 208 removed outlier: 9.114A pdb=" N LEU F 245 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP F 205 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL F 247 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 207 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS F 249 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR F 225 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 121 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 222 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 132 through 140 Processing sheet with id=AE4, first strand: chain 'F' and resid 311 through 312 removed outlier: 3.561A pdb=" N ARG F 311 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 349 through 353 removed outlier: 6.016A pdb=" N ILE F 350 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP F 393 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR F 352 " --> pdb=" O ASP F 393 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 390 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA F 435 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE F 392 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL F 325 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU F 326 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU F 469 " --> pdb=" O LEU F 326 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL F 328 " --> pdb=" O LEU F 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.923A pdb=" N ALA F 365 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU F 378 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 414 through 417 removed outlier: 3.878A pdb=" N ILE F 417 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 519 through 520 removed outlier: 6.903A pdb=" N VAL F 519 " --> pdb=" O VAL F 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 1033 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.00 Time building geometry restraints manager: 12.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9714 1.34 - 1.46: 5341 1.46 - 1.58: 14051 1.58 - 1.70: 22 1.70 - 1.82: 142 Bond restraints: 29270 Sorted by residual: bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP A 702 " pdb=" C5 ATP A 702 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP D 702 " pdb=" C5 ATP D 702 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C4 ATP C 702 " pdb=" C5 ATP C 702 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.31e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.30e+01 ... (remaining 29265 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.62: 1103 107.62 - 114.75: 18011 114.75 - 121.87: 14337 121.87 - 128.99: 6125 128.99 - 136.12: 134 Bond angle restraints: 39710 Sorted by residual: angle pdb=" PB ATP D 702 " pdb=" O3B ATP D 702 " pdb=" PG ATP D 702 " ideal model delta sigma weight residual 139.87 116.65 23.22 1.00e+00 1.00e+00 5.39e+02 angle pdb=" PA ATP E 701 " pdb=" O3A ATP E 701 " pdb=" PB ATP E 701 " ideal model delta sigma weight residual 136.83 114.02 22.81 1.00e+00 1.00e+00 5.20e+02 angle pdb=" PA ATP A 702 " pdb=" O3A ATP A 702 " pdb=" PB ATP A 702 " ideal model delta sigma weight residual 136.83 117.48 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 117.82 19.01 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP C 702 " pdb=" O3A ATP C 702 " pdb=" PB ATP C 702 " ideal model delta sigma weight residual 136.83 117.82 19.01 1.00e+00 1.00e+00 3.61e+02 ... (remaining 39705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 16947 17.54 - 35.08: 1010 35.08 - 52.62: 172 52.62 - 70.16: 44 70.16 - 87.70: 17 Dihedral angle restraints: 18190 sinusoidal: 7025 harmonic: 11165 Sorted by residual: dihedral pdb=" CA ASP A 190 " pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " pdb=" OD1 ASP A 190 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 174 " pdb=" CB ASP D 174 " pdb=" CG ASP D 174 " pdb=" OD1 ASP D 174 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 386 " pdb=" CB ASP C 386 " pdb=" CG ASP C 386 " pdb=" OD1 ASP C 386 " ideal model delta sinusoidal sigma weight residual -30.00 -88.99 58.99 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 18187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3109 0.031 - 0.061: 1030 0.061 - 0.092: 401 0.092 - 0.122: 199 0.122 - 0.153: 23 Chirality restraints: 4762 Sorted by residual: chirality pdb=" CB ILE C 291 " pdb=" CA ILE C 291 " pdb=" CG1 ILE C 291 " pdb=" CG2 ILE C 291 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ASP F 278 " pdb=" N ASP F 278 " pdb=" C ASP F 278 " pdb=" CB ASP F 278 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CB ILE A 231 " pdb=" CA ILE A 231 " pdb=" CG1 ILE A 231 " pdb=" CG2 ILE A 231 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 4759 not shown) Planarity restraints: 5094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 238 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO C 239 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 239 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 239 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 130 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO F 131 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 131 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 131 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 548 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO F 549 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO F 549 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 549 " -0.018 5.00e-02 4.00e+02 ... (remaining 5091 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 293 2.62 - 3.19: 26002 3.19 - 3.76: 45758 3.76 - 4.33: 63430 4.33 - 4.90: 100812 Nonbonded interactions: 236295 Sorted by model distance: nonbonded pdb="MG MG A 701 " pdb=" O1B ATP A 702 " model vdw 2.050 2.170 nonbonded pdb=" CG GLU F 411 " pdb=" OE1 GLN F 412 " model vdw 2.154 3.440 nonbonded pdb=" OG SER D 336 " pdb="MG MG D 701 " model vdw 2.194 2.170 nonbonded pdb=" O VAL F 610 " pdb=" OG SER F 614 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR F 508 " pdb=" O MET F 570 " model vdw 2.274 3.040 ... (remaining 236290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 13 or resid 27 through 54 or (resid 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 through 71 or (resid \ 72 through 74 and (name N or name CA or name C or name O or name CB )) or resid \ 75 through 89 or (resid 90 through 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 through 140 or (resid 141 through 142 and (name N or \ name CA or name C or name O or name CB )) or resid 143 through 151 or (resid 15 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 163 or (resid 164 through 165 and (name N or name CA or name C or name O or name \ CB )) or resid 166 through 186 or (resid 187 and (name N or name CA or name C o \ r name O or name CB )) or resid 188 through 194 or (resid 195 and (name N or nam \ e CA or name C or name O or name CB )) or resid 196 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 213 \ or (resid 214 through 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 219 or (resid 220 through 221 and (name N or name CA or \ name C or name O or name CB )) or resid 222 through 232 or (resid 233 through 23 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 239 through \ 240 or (resid 241 and (name N or name CA or name C or name O or name CB )) or re \ sid 242 or (resid 243 and (name N or name CA or name C or name O or name CB )) o \ r resid 244 through 250 or (resid 251 and (name N or name CA or name C or name O \ or name CB )) or resid 252 through 254 or (resid 255 through 256 and (name N or \ name CA or name C or name O or name CB )) or resid 257 or (resid 258 through 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 or (resi \ d 261 through 262 and (name N or name CA or name C or name O or name CB )) or re \ sid 263 through 264 or (resid 265 through 267 and (name N or name CA or name C o \ r name O or name CB )) or resid 268 through 314 or (resid 315 and (name N or nam \ e CA or name C or name O or name CB )) or resid 316 through 350 or (resid 351 an \ d (name N or name CA or name C or name O or name CB )) or resid 352 through 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 392 or (resid 393 through 394 and (name N or name CA or \ name C or name O or name CB )) or resid 395 through 399 or (resid 400 and (name \ N or name CA or name C or name O or name CB )) or resid 401 through 445 or (resi \ d 446 and (name N or name CA or name C or name O or name CB )) or resid 447 thro \ ugh 473 or (resid 474 through 475 and (name N or name CA or name C or name O or \ name CB )) or resid 476 through 482 or (resid 483 and (name N or name CA or name \ C or name O or name CB )) or resid 484 through 491 or (resid 492 through 495 an \ d (name N or name CA or name C or name O or name CB )) or resid 496 through 536 \ or (resid 537 and (name N or name CA or name C or name O or name CB )) or resid \ 538 or (resid 539 through 541 and (name N or name CA or name C or name O or name \ CB )) or resid 542 through 547 or (resid 548 and (name N or name CA or name C o \ r name O or name CB )) or resid 549 through 595)) selection = (chain 'B' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 31 or (resid \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 through \ 65 or (resid 66 through 67 and (name N or name CA or name C or name O or name C \ B )) or resid 68 through 71 or (resid 72 through 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 80 through 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 89 or ( \ resid 90 through 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 148 or (resid 1 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 150 through \ 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or r \ esid 153 through 163 or (resid 164 through 165 and (name N or name CA or name C \ or name O or name CB )) or resid 166 through 186 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 219 or (resid 220 through 221 and (name N or name CA or name C or n \ ame O or name CB )) or resid 222 through 232 or (resid 233 through 238 and (name \ N or name CA or name C or name O or name CB )) or resid 239 or (resid 240 throu \ gh 241 and (name N or name CA or name C or name O or name CB )) or resid 242 or \ (resid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 \ through 250 or (resid 251 and (name N or name CA or name C or name O or name CB \ )) or resid 252 through 254 or (resid 255 through 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 or (resid 258 through 259 and (name \ N or name CA or name C or name O or name CB )) or resid 260 or (resid 261 throu \ gh 262 and (name N or name CA or name C or name O or name CB )) or resid 263 thr \ ough 264 or (resid 265 through 267 and (name N or name CA or name C or name O or \ name CB )) or resid 268 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 or (resid 317 and (name N or name CA or \ name C or name O or name CB )) or resid 318 through 350 or (resid 351 and (name \ N or name CA or name C or name O or name CB )) or resid 352 through 368 or (res \ id 369 through 371 and (name N or name CA or name C or name O or name CB )) or r \ esid 372 through 392 or (resid 393 through 394 and (name N or name CA or name C \ or name O or name CB )) or resid 395 through 399 or (resid 400 and (name N or na \ me CA or name C or name O or name CB )) or resid 401 through 407 or (resid 408 t \ hrough 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ or (resid 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 421 or (resid 422 and (name N or name CA or name C or name O or nam \ e CB )) or resid 423 through 445 or (resid 446 and (name N or name CA or name C \ or name O or name CB )) or resid 447 through 450 or (resid 451 and (name N or na \ me CA or name C or name O or name CB )) or resid 452 through 453 or (resid 454 a \ nd (name N or name CA or name C or name O or name CB )) or resid 455 through 461 \ or (resid 462 and (name N or name CA or name C or name O or name CB )) or resid \ 463 through 474 or (resid 475 and (name N or name CA or name C or name O or nam \ e CB )) or resid 476 through 477 or (resid 478 through 479 and (name N or name C \ A or name C or name O or name CB )) or resid 480 through 482 or (resid 483 and ( \ name N or name CA or name C or name O or name CB )) or resid 484 through 491 or \ (resid 492 through 495 and (name N or name CA or name C or name O or name CB )) \ or resid 496 through 502 or (resid 503 and (name N or name CA or name C or name \ O or name CB )) or resid 504 through 535 or (resid 536 through 537 and (name N o \ r name CA or name C or name O or name CB )) or (resid 538 through 545 and (name \ N or name CA or name C or name O or name CB )) or resid 546 through 547 or (resi \ d 548 and (name N or name CA or name C or name O or name CB )) or resid 549 or ( \ resid 550 and (name N or name CA or name C or name O or name CB )) or resid 551 \ through 557 or (resid 558 through 559 and (name N or name CA or name C or name O \ or name CB )) or resid 560 through 564 or (resid 565 through 566 and (name N or \ name CA or name C or name O or name CB )) or resid 567 through 579 or (resid 58 \ 0 through 581 and (name N or name CA or name C or name O or name CB )) or resid \ 582 through 585 or (resid 586 and (name N or name CA or name C or name O or name \ CB )) or resid 587 through 595)) selection = (chain 'C' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 through \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 through \ 65 or (resid 66 through 67 and (name N or name CA or name C or name O or name C \ B )) or resid 68 through 71 or (resid 72 through 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 80 through 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 89 or ( \ resid 90 through 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 through 140 or (resid 141 through 142 a \ nd (name N or name CA or name C or name O or name CB )) or resid 143 through 145 \ or (resid 146 and (name N or name CA or name C or name O or name CB )) or resid \ 147 through 148 or (resid 149 and (name N or name CA or name C or name O or nam \ e CB )) or resid 150 through 163 or (resid 164 through 165 and (name N or name C \ A or name C or name O or name CB )) or resid 166 through 186 or (resid 187 and ( \ name N or name CA or name C or name O or name CB )) or resid 188 through 194 or \ (resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 199 or (resid 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 213 or (resid 214 through 216 and (name N or name CA or \ name C or name O or name CB )) or resid 217 through 219 or (resid 220 through 2 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 233 or (resid 234 through 238 and (name N or name CA or name C or name O or nam \ e CB )) or resid 239 or (resid 240 through 241 and (name N or name CA or name C \ or name O or name CB )) or resid 242 or (resid 243 and (name N or name CA or nam \ e C or name O or name CB )) or resid 244 through 250 or (resid 251 and (name N o \ r name CA or name C or name O or name CB )) or resid 252 through 254 or (resid 2 \ 55 through 256 and (name N or name CA or name C or name O or name CB )) or resid \ 257 or (resid 258 through 259 and (name N or name CA or name C or name O or nam \ e CB )) or resid 260 or (resid 261 through 262 and (name N or name CA or name C \ or name O or name CB )) or resid 263 through 265 or (resid 266 through 267 and ( \ name N or name CA or name C or name O or name CB )) or resid 268 through 314 or \ (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ or (resid 317 and (name N or name CA or name C or name O or name CB )) or resid \ 318 through 350 or (resid 351 and (name N or name CA or name C or name O or nam \ e CB )) or resid 352 through 368 or (resid 369 through 371 and (name N or name C \ A or name C or name O or name CB )) or resid 372 through 392 or (resid 393 throu \ gh 394 and (name N or name CA or name C or name O or name CB )) or resid 395 thr \ ough 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 407 or (resid 408 through 409 and (name N or name CA or nam \ e C or name O or name CB )) or resid 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 418 or (resid 419 through 4 \ 20 and (name N or name CA or name C or name O or name CB )) or resid 421 or (res \ id 422 and (name N or name CA or name C or name O or name CB )) or resid 423 thr \ ough 445 or (resid 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 through 450 or (resid 451 and (name N or name CA or name C or name \ O or name CB )) or resid 452 through 453 or (resid 454 and (name N or name CA or \ name C or name O or name CB )) or resid 455 through 461 or (resid 462 and (name \ N or name CA or name C or name O or name CB )) or resid 463 through 473 or (res \ id 474 through 475 and (name N or name CA or name C or name O or name CB )) or r \ esid 476 through 477 or (resid 478 through 479 and (name N or name CA or name C \ or name O or name CB )) or resid 480 through 482 or (resid 483 and (name N or na \ me CA or name C or name O or name CB )) or resid 484 through 491 or (resid 492 t \ hrough 495 and (name N or name CA or name C or name O or name CB )) or resid 496 \ through 502 or (resid 503 and (name N or name CA or name C or name O or name CB \ )) or resid 504 through 535 or (resid 536 through 537 and (name N or name CA or \ name C or name O or name CB )) or resid 538 or (resid 539 through 541 and (name \ N or name CA or name C or name O or name CB )) or (resid 542 through 545 and (n \ ame N or name CA or name C or name O or name CB )) or resid 546 through 549 or ( \ resid 550 and (name N or name CA or name C or name O or name CB )) or resid 551 \ through 557 or (resid 558 through 559 and (name N or name CA or name C or name O \ or name CB )) or resid 560 through 564 or (resid 565 through 566 and (name N or \ name CA or name C or name O or name CB )) or resid 567 through 579 or (resid 58 \ 0 through 581 and (name N or name CA or name C or name O or name CB )) or resid \ 582 through 585 or (resid 586 and (name N or name CA or name C or name O or name \ CB )) or resid 587 through 595)) selection = (chain 'D' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 54 or (resid \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 65 or (resid 66 through 67 and (name N or name CA or name C or name O or name C \ B )) or resid 68 through 71 or (resid 72 through 74 and (name N or name CA or na \ me C or name O or name CB )) or resid 75 through 79 or (resid 80 through 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 89 or ( \ resid 90 through 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 148 or (resid 1 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 150 through \ 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or r \ esid 153 through 163 or (resid 164 through 165 and (name N or name CA or name C \ or name O or name CB )) or resid 166 through 194 or (resid 195 and (name N or na \ me CA or name C or name O or name CB )) or resid 196 through 213 or (resid 214 t \ hrough 216 and (name N or name CA or name C or name O or name CB )) or resid 217 \ through 219 or (resid 220 through 221 and (name N or name CA or name C or name \ O or name CB )) or resid 222 through 232 or (resid 233 through 238 and (name N o \ r name CA or name C or name O or name CB )) or resid 239 or (resid 240 through 2 \ 41 and (name N or name CA or name C or name O or name CB )) or resid 242 or (res \ id 243 and (name N or name CA or name C or name O or name CB )) or resid 244 thr \ ough 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 254 or (resid 255 through 256 and (name N or name CA or nam \ e C or name O or name CB )) or resid 257 or (resid 258 through 259 and (name N o \ r name CA or name C or name O or name CB )) or resid 260 or (resid 261 through 2 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 263 through \ 264 or (resid 265 through 267 and (name N or name CA or name C or name O or nam \ e CB )) or resid 268 through 314 or (resid 315 and (name N or name CA or name C \ or name O or name CB )) or resid 316 or (resid 317 and (name N or name CA or nam \ e C or name O or name CB )) or resid 318 through 350 or (resid 351 and (name N o \ r name CA or name C or name O or name CB )) or resid 352 through 367 or (resid 3 \ 68 through 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 392 or (resid 393 through 394 and (name N or name CA or name C or n \ ame O or name CB )) or resid 395 through 399 or (resid 400 and (name N or name C \ A or name C or name O or name CB )) or resid 401 through 407 or (resid 408 throu \ gh 409 and (name N or name CA or name C or name O or name CB )) or resid 410 or \ (resid 411 and (name N or name CA or name C or name O or name CB )) or resid 412 \ through 421 or (resid 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 445 or (resid 446 and (name N or name CA or name C or n \ ame O or name CB )) or resid 447 through 450 or (resid 451 and (name N or name C \ A or name C or name O or name CB )) or resid 452 through 453 or (resid 454 and ( \ name N or name CA or name C or name O or name CB )) or resid 455 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 473 or (resid 474 through 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 477 or (resid 478 through 479 and (name N o \ r name CA or name C or name O or name CB )) or resid 480 through 482 or (resid 4 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 484 through \ 491 or (resid 492 through 495 and (name N or name CA or name C or name O or nam \ e CB )) or resid 496 through 502 or (resid 503 and (name N or name CA or name C \ or name O or name CB )) or resid 504 through 535 or (resid 536 through 537 and ( \ name N or name CA or name C or name O or name CB )) or resid 538 or (resid 539 t \ hrough 541 and (name N or name CA or name C or name O or name CB )) or (resid 54 \ 2 through 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 547 or (resid 548 and (name N or name CA or name C or name O or name \ CB )) or resid 549 or (resid 550 and (name N or name CA or name C or name O or \ name CB )) or resid 551 through 557 or (resid 558 through 559 and (name N or nam \ e CA or name C or name O or name CB )) or resid 560 through 564 or (resid 565 th \ rough 566 and (name N or name CA or name C or name O or name CB )) or resid 567 \ through 579 or (resid 580 through 581 and (name N or name CA or name C or name O \ or name CB )) or resid 582 through 585 or (resid 586 and (name N or name CA or \ name C or name O or name CB )) or resid 587 through 595)) selection = (chain 'E' and (resid 1 through 13 or resid 27 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 31 or (resid \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 through \ 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or res \ id 56 through 65 or (resid 66 through 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 through 71 or (resid 72 through 74 and (name N or \ name CA or name C or name O or name CB )) or resid 75 through 106 or (resid 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 through 13 \ 3 or (resid 134 and (name N or name CA or name C or name O or name CB )) or resi \ d 135 through 140 or (resid 141 through 142 and (name N or name CA or name C or \ name O or name CB )) or resid 143 through 151 or (resid 152 and (name N or name \ CA or name C or name O or name CB )) or resid 153 through 155 or (resid 156 and \ (name N or name CA or name C or name O or name CB )) or resid 157 through 199 or \ (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 1 through 213 or (resid 214 through 216 and (name N or name CA or name C or name \ O or name CB )) or resid 217 through 219 or (resid 220 through 221 and (name N \ or name CA or name C or name O or name CB )) or resid 222 through 233 or (resid \ 234 through 238 and (name N or name CA or name C or name O or name CB )) or resi \ d 239 through 240 or (resid 241 and (name N or name CA or name C or name O or na \ me CB )) or resid 242 or (resid 243 and (name N or name CA or name C or name O o \ r name CB )) or resid 244 through 250 or (resid 251 and (name N or name CA or na \ me C or name O or name CB )) or resid 252 through 255 or (resid 256 and (name N \ or name CA or name C or name O or name CB )) or resid 257 or (resid 258 through \ 259 and (name N or name CA or name C or name O or name CB )) or resid 260 throug \ h 261 or (resid 262 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 264 or (resid 265 through 267 and (name N or name CA or name C \ or name O or name CB )) or resid 268 through 314 or (resid 315 and (name N or n \ ame CA or name C or name O or name CB )) or resid 316 or (resid 317 and (name N \ or name CA or name C or name O or name CB )) or resid 318 through 350 or (resid \ 351 and (name N or name CA or name C or name O or name CB )) or resid 352 throug \ h 368 or (resid 369 through 371 and (name N or name CA or name C or name O or na \ me CB )) or resid 372 through 392 or (resid 393 through 394 and (name N or name \ CA or name C or name O or name CB )) or resid 395 through 399 or (resid 400 and \ (name N or name CA or name C or name O or name CB )) or resid 401 through 407 or \ (resid 408 through 409 and (name N or name CA or name C or name O or name CB )) \ or resid 410 or (resid 411 and (name N or name CA or name C or name O or name C \ B )) or resid 412 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 450 or (resid 451 and (name N or name \ CA or name C or name O or name CB )) or resid 452 through 453 or (resid 454 and \ (name N or name CA or name C or name O or name CB )) or resid 455 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 through 473 or (resid 474 through 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 477 or (resid 478 through 479 and (name N \ or name CA or name C or name O or name CB )) or resid 480 through 491 or (resid \ 492 through 495 and (name N or name CA or name C or name O or name CB )) or resi \ d 496 through 535 or (resid 536 through 537 and (name N or name CA or name C or \ name O or name CB )) or resid 538 or (resid 539 through 541 and (name N or name \ CA or name C or name O or name CB )) or (resid 542 through 545 and (name N or na \ me CA or name C or name O or name CB )) or resid 546 through 547 or (resid 548 a \ nd (name N or name CA or name C or name O or name CB )) or resid 549 or (resid 5 \ 50 and (name N or name CA or name C or name O or name CB )) or resid 551 through \ 557 or (resid 558 through 559 and (name N or name CA or name C or name O or nam \ e CB )) or resid 560 through 564 or (resid 565 through 566 and (name N or name C \ A or name C or name O or name CB )) or resid 567 through 579 or (resid 580 throu \ gh 581 and (name N or name CA or name C or name O or name CB )) or resid 582 thr \ ough 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 595)) selection = (chain 'F' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 86 or (resid 87 through 91 and (nam \ e N or name CA or name C or name O or name CB )) or resid 92 through 106 or (res \ id 107 and (name N or name CA or name C or name O or name CB )) or resid 108 thr \ ough 140 or (resid 141 through 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 148 or (resid 149 and (name N o \ r name CA or name C or name O or name CB )) or resid 150 through 151 or (resid 1 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) or r \ esid 173 through 186 or (resid 187 and (name N or name CA or name C or name O or \ name CB )) or resid 188 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 199 or (resid 200 and (name N o \ r name CA or name C or name O or name CB )) or resid 201 through 213 or (resid 2 \ 14 through 216 and (name N or name CA or name C or name O or name CB )) or resid \ 217 through 220 or (resid 221 and (name N or name CA or name C or name O or nam \ e CB )) or resid 222 through 233 or (resid 234 through 238 and (name N or name C \ A or name C or name O or name CB )) or resid 239 or (resid 240 through 241 and ( \ name N or name CA or name C or name O or name CB )) or resid 242 through 254 or \ (resid 255 through 256 and (name N or name CA or name C or name O or name CB )) \ or resid 257 through 260 or (resid 261 through 262 and (name N or name CA or nam \ e C or name O or name CB )) or resid 263 through 265 or (resid 266 through 267 a \ nd (name N or name CA or name C or name O or name CB )) or resid 268 through 368 \ or (resid 369 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 407 or (resid 408 through 409 and (name N or name CA or \ name C or name O or name CB )) or resid 410 or (resid 411 and (name N or name C \ A or name C or name O or name CB )) or resid 412 through 421 or (resid 422 and ( \ name N or name CA or name C or name O or name CB )) or resid 423 through 445 or \ (resid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ through 450 or (resid 451 and (name N or name CA or name C or name O or name CB \ )) or resid 452 through 453 or (resid 454 and (name N or name CA or name C or n \ ame O or name CB )) or resid 455 through 461 or (resid 462 and (name N or name C \ A or name C or name O or name CB )) or resid 463 through 473 or (resid 474 throu \ gh 475 and (name N or name CA or name C or name O or name CB )) or resid 476 thr \ ough 477 or (resid 478 through 479 and (name N or name CA or name C or name O or \ name CB )) or resid 480 through 535 or (resid 536 through 537 and (name N or na \ me CA or name C or name O or name CB )) or resid 538 or (resid 539 through 541 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 542 through 54 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 546 through \ 547 or (resid 548 and (name N or name CA or name C or name O or name CB )) or re \ sid 549 or (resid 550 and (name N or name CA or name C or name O or name CB )) o \ r resid 551 through 557 or (resid 558 through 559 and (name N or name CA or name \ C or name O or name CB )) or resid 560 through 564 or (resid 565 through 566 an \ d (name N or name CA or name C or name O or name CB )) or resid 567 through 579 \ or (resid 580 through 581 and (name N or name CA or name C or name O or name CB \ )) or resid 582 through 585 or (resid 586 and (name N or name CA or name C or na \ me O or name CB )) or resid 587 through 595)) } 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 group one per residue 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 75.360 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 : 0.003 0.132 29270 Z= 0.201 Angle : 0.663 23.224 39710 Z= 0.469 Chirality : 0.040 0.153 4762 Planarity : 0.003 0.078 5094 Dihedral : 11.875 87.697 10904 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.52 % Favored : 97.37 % Rotamer: Outliers : 0.31 % Allowed : 3.10 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.11), residues: 3806 helix: -2.60 (0.10), residues: 1423 sheet: -2.96 (0.16), residues: 670 loop : -1.99 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 46 HIS 0.003 0.000 HIS F 249 PHE 0.008 0.001 PHE D 132 TYR 0.012 0.001 TYR D 508 ARG 0.003 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 427 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7410 (mpt-90) cc_final: 0.6433 (mmm160) REVERT: D 202 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5637 (mpp80) REVERT: D 246 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7058 (tm-30) REVERT: D 255 LYS cc_start: 0.7368 (mmmt) cc_final: 0.6525 (mmmt) REVERT: D 355 LYS cc_start: 0.7568 (mmtm) cc_final: 0.7310 (mmtp) REVERT: D 483 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7390 (tm-30) REVERT: D 612 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8288 (tttt) REVERT: C 46 TRP cc_start: 0.8317 (t60) cc_final: 0.7942 (t60) REVERT: C 119 VAL cc_start: 0.8985 (p) cc_final: 0.8652 (m) REVERT: C 470 LEU cc_start: 0.8259 (tp) cc_final: 0.8059 (tt) REVERT: B 525 MET cc_start: 0.8228 (mtp) cc_final: 0.8002 (mtp) REVERT: B 552 ILE cc_start: 0.8145 (tt) cc_final: 0.6998 (tt) REVERT: B 570 MET cc_start: 0.8831 (ttp) cc_final: 0.8625 (ttm) REVERT: E 52 PHE cc_start: 0.6874 (t80) cc_final: 0.6413 (m-80) REVERT: E 200 MET cc_start: 0.1746 (mmp) cc_final: 0.1325 (ptt) REVERT: E 217 LEU cc_start: 0.8103 (mm) cc_final: 0.7271 (mm) REVERT: A 1 MET cc_start: 0.6643 (ptp) cc_final: 0.6051 (pmm) REVERT: A 195 LEU cc_start: 0.7904 (mp) cc_final: 0.7459 (tp) REVERT: F 42 LEU cc_start: 0.7233 (tt) cc_final: 0.6723 (tp) REVERT: F 525 MET cc_start: 0.7772 (mtp) cc_final: 0.7383 (mtt) REVERT: F 548 GLN cc_start: 0.6609 (tp-100) cc_final: 0.6094 (tm-30) REVERT: F 572 LEU cc_start: 0.8457 (mt) cc_final: 0.8027 (mt) REVERT: F 591 MET cc_start: 0.8428 (tmm) cc_final: 0.7517 (tmm) REVERT: F 592 MET cc_start: 0.7471 (mmm) cc_final: 0.7182 (mmm) outliers start: 9 outliers final: 3 residues processed: 434 average time/residue: 0.5126 time to fit residues: 323.8176 Evaluate side-chains 240 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 318 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 6.9990 chunk 289 optimal weight: 20.0000 chunk 160 optimal weight: 0.0040 chunk 98 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 HIS D 344 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 294 HIS C 412 GLN C 649 GLN B 199 GLN B 344 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 98 ASN E 151 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN E 618 ASN A 170 ASN A 344 ASN A 407 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29270 Z= 0.279 Angle : 0.594 9.741 39710 Z= 0.302 Chirality : 0.043 0.169 4762 Planarity : 0.004 0.044 5094 Dihedral : 7.060 85.112 4295 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.03 % Rotamer: Outliers : 1.84 % Allowed : 9.57 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.12), residues: 3806 helix: -0.78 (0.12), residues: 1472 sheet: -2.61 (0.18), residues: 640 loop : -1.63 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 46 HIS 0.006 0.001 HIS B 294 PHE 0.018 0.002 PHE D 443 TYR 0.024 0.002 TYR B 531 ARG 0.009 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 247 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.7615 (ttmm) cc_final: 0.7391 (ttmm) REVERT: D 152 ARG cc_start: 0.7475 (mpt-90) cc_final: 0.6505 (mmm160) REVERT: D 202 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5932 (mpp80) REVERT: D 241 PHE cc_start: 0.6731 (m-80) cc_final: 0.6229 (m-80) REVERT: D 246 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 355 LYS cc_start: 0.7532 (mmtm) cc_final: 0.7280 (mmtp) REVERT: D 483 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7492 (tm-30) REVERT: D 612 LYS cc_start: 0.8564 (ttmt) cc_final: 0.7964 (pttp) REVERT: C 225 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8650 (t) REVERT: B 552 ILE cc_start: 0.7792 (tt) cc_final: 0.6478 (tt) REVERT: E 52 PHE cc_start: 0.7175 (t80) cc_final: 0.6960 (m-80) REVERT: E 200 MET cc_start: 0.2160 (mmp) cc_final: 0.1335 (ptt) REVERT: E 225 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8615 (t) REVERT: E 340 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7494 (mmt90) REVERT: A 1 MET cc_start: 0.7119 (ptp) cc_final: 0.6461 (pmm) REVERT: A 535 MET cc_start: 0.8955 (mtp) cc_final: 0.8684 (mtp) REVERT: F 42 LEU cc_start: 0.7315 (tt) cc_final: 0.6850 (tp) REVERT: F 303 LEU cc_start: 0.8056 (mt) cc_final: 0.7769 (mp) REVERT: F 398 MET cc_start: 0.7397 (mmm) cc_final: 0.7176 (mmm) REVERT: F 548 GLN cc_start: 0.6506 (tp-100) cc_final: 0.6066 (tm-30) REVERT: F 591 MET cc_start: 0.8729 (tmm) cc_final: 0.7844 (tmm) REVERT: F 592 MET cc_start: 0.7685 (mmm) cc_final: 0.7397 (mmm) outliers start: 53 outliers final: 27 residues processed: 288 average time/residue: 0.4312 time to fit residues: 196.2777 Evaluate side-chains 233 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 375 optimal weight: 0.6980 chunk 309 optimal weight: 10.0000 chunk 344 optimal weight: 0.1980 chunk 118 optimal weight: 0.7980 chunk 278 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS D 437 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 GLN F 437 ASN F 446 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29270 Z= 0.200 Angle : 0.529 10.486 39710 Z= 0.266 Chirality : 0.042 0.163 4762 Planarity : 0.004 0.040 5094 Dihedral : 6.845 88.889 4291 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.05 % Allowed : 12.00 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 3806 helix: 0.04 (0.13), residues: 1470 sheet: -2.48 (0.18), residues: 624 loop : -1.32 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 46 HIS 0.004 0.001 HIS A 567 PHE 0.017 0.001 PHE D 10 TYR 0.019 0.002 TYR B 531 ARG 0.007 0.000 ARG E 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 224 time to evaluate : 3.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.7550 (ttmm) cc_final: 0.7345 (mttp) REVERT: D 152 ARG cc_start: 0.7498 (mpt-90) cc_final: 0.6519 (mmm160) REVERT: D 202 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6191 (mpp80) REVERT: D 241 PHE cc_start: 0.6863 (m-80) cc_final: 0.6283 (m-80) REVERT: D 246 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7405 (tm-30) REVERT: D 355 LYS cc_start: 0.7545 (mmtm) cc_final: 0.7330 (mmtp) REVERT: D 483 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7459 (tm-30) REVERT: D 612 LYS cc_start: 0.8575 (ttmt) cc_final: 0.7925 (pttp) REVERT: C 189 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: C 225 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8644 (t) REVERT: C 488 VAL cc_start: 0.8753 (t) cc_final: 0.8410 (p) REVERT: B 10 PHE cc_start: 0.7518 (m-80) cc_final: 0.7315 (m-80) REVERT: B 525 MET cc_start: 0.8161 (mtp) cc_final: 0.7474 (mtm) REVERT: B 535 MET cc_start: 0.8419 (mmm) cc_final: 0.8109 (mmm) REVERT: E 200 MET cc_start: 0.2260 (mmp) cc_final: 0.1341 (ptt) REVERT: E 225 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8626 (t) REVERT: E 340 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7511 (mmt90) REVERT: E 369 ASP cc_start: 0.6386 (p0) cc_final: 0.6122 (t70) REVERT: A 1 MET cc_start: 0.7142 (ptp) cc_final: 0.6492 (pmm) REVERT: A 195 LEU cc_start: 0.7894 (mt) cc_final: 0.7382 (tp) REVERT: A 535 MET cc_start: 0.9052 (mtp) cc_final: 0.8802 (mtp) REVERT: A 591 MET cc_start: 0.7091 (tmm) cc_final: 0.6103 (tmm) REVERT: F 42 LEU cc_start: 0.7255 (tt) cc_final: 0.6777 (tp) REVERT: F 548 GLN cc_start: 0.6498 (tp-100) cc_final: 0.5905 (tm-30) outliers start: 59 outliers final: 32 residues processed: 271 average time/residue: 0.4022 time to fit residues: 174.7187 Evaluate side-chains 231 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 233 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 369 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 437 ASN B 515 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 444 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 29270 Z= 0.473 Angle : 0.685 9.151 39710 Z= 0.344 Chirality : 0.046 0.184 4762 Planarity : 0.005 0.084 5094 Dihedral : 7.202 85.262 4291 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 2.68 % Allowed : 14.30 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3806 helix: 0.12 (0.14), residues: 1473 sheet: -2.49 (0.19), residues: 619 loop : -1.37 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 375 HIS 0.009 0.002 HIS B 294 PHE 0.022 0.002 PHE E 183 TYR 0.021 0.002 TYR D 532 ARG 0.031 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 197 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.7624 (ttmm) cc_final: 0.7415 (mttm) REVERT: D 152 ARG cc_start: 0.7640 (mpt-90) cc_final: 0.6729 (mmm160) REVERT: D 202 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6582 (mpt-90) REVERT: D 241 PHE cc_start: 0.6864 (m-80) cc_final: 0.6494 (m-80) REVERT: D 612 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8030 (pttp) REVERT: C 225 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8829 (t) REVERT: C 476 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8070 (tttm) REVERT: C 603 LEU cc_start: 0.5634 (mt) cc_final: 0.5358 (pt) REVERT: A 1 MET cc_start: 0.7188 (ptp) cc_final: 0.6485 (pmm) REVERT: A 195 LEU cc_start: 0.7961 (mt) cc_final: 0.7509 (tp) REVERT: A 233 GLU cc_start: 0.8186 (mp0) cc_final: 0.7984 (mp0) REVERT: A 592 MET cc_start: 0.8235 (mpp) cc_final: 0.8010 (mpp) REVERT: F 200 MET cc_start: 0.4036 (tpt) cc_final: 0.3112 (ttt) outliers start: 77 outliers final: 45 residues processed: 259 average time/residue: 0.4296 time to fit residues: 183.2993 Evaluate side-chains 223 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 175 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 553 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 5.9990 chunk 209 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 152 optimal weight: 0.0970 chunk 315 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 2.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN B 407 HIS B 556 GLN E 50 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29270 Z= 0.359 Angle : 0.608 10.025 39710 Z= 0.304 Chirality : 0.044 0.164 4762 Planarity : 0.004 0.048 5094 Dihedral : 7.079 82.990 4291 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 2.99 % Allowed : 15.76 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3806 helix: 0.26 (0.14), residues: 1498 sheet: -2.42 (0.19), residues: 589 loop : -1.35 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 375 HIS 0.005 0.001 HIS B 294 PHE 0.021 0.002 PHE D 10 TYR 0.020 0.002 TYR F 97 ARG 0.008 0.001 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 183 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.6965 (p0) REVERT: D 152 ARG cc_start: 0.7666 (mpt-90) cc_final: 0.6745 (mmm160) REVERT: D 202 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6353 (mpt-90) REVERT: D 241 PHE cc_start: 0.7019 (m-80) cc_final: 0.6453 (m-80) REVERT: D 612 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8048 (pttp) REVERT: C 476 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7978 (tttm) REVERT: C 488 VAL cc_start: 0.8710 (t) cc_final: 0.8419 (p) REVERT: B 425 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 1 MET cc_start: 0.7077 (ptp) cc_final: 0.6409 (pmm) REVERT: A 195 LEU cc_start: 0.7995 (mt) cc_final: 0.7580 (tp) REVERT: F 42 LEU cc_start: 0.7049 (tt) cc_final: 0.6826 (tp) REVERT: F 97 TYR cc_start: 0.8003 (p90) cc_final: 0.7518 (p90) REVERT: F 398 MET cc_start: 0.7505 (mmm) cc_final: 0.7292 (mmm) REVERT: F 588 ILE cc_start: 0.7067 (tp) cc_final: 0.6866 (tp) outliers start: 86 outliers final: 51 residues processed: 253 average time/residue: 0.3680 time to fit residues: 154.3608 Evaluate side-chains 227 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 553 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 0.8980 chunk 332 optimal weight: 0.1980 chunk 72 optimal weight: 0.0670 chunk 216 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 29270 Z= 0.165 Angle : 0.531 11.062 39710 Z= 0.267 Chirality : 0.042 0.173 4762 Planarity : 0.004 0.044 5094 Dihedral : 6.729 83.135 4291 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Rotamer: Outliers : 2.12 % Allowed : 17.22 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3806 helix: 0.62 (0.14), residues: 1482 sheet: -2.34 (0.19), residues: 586 loop : -1.13 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 375 HIS 0.017 0.001 HIS B 407 PHE 0.022 0.001 PHE D 10 TYR 0.021 0.001 TYR F 531 ARG 0.006 0.000 ARG F 522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 189 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7706 (mpt-90) cc_final: 0.6748 (mmm160) REVERT: D 612 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8045 (pttp) REVERT: C 92 VAL cc_start: 0.6025 (OUTLIER) cc_final: 0.5696 (p) REVERT: C 422 ILE cc_start: 0.7577 (mm) cc_final: 0.7374 (tp) REVERT: C 470 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8475 (mp) REVERT: C 488 VAL cc_start: 0.8637 (t) cc_final: 0.8323 (p) REVERT: A 1 MET cc_start: 0.7123 (ptp) cc_final: 0.6381 (pmm) REVERT: A 195 LEU cc_start: 0.8024 (mt) cc_final: 0.7625 (tp) REVERT: F 40 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.5833 (ttp-170) REVERT: F 42 LEU cc_start: 0.6909 (tt) cc_final: 0.6690 (tp) REVERT: F 97 TYR cc_start: 0.7936 (p90) cc_final: 0.7303 (p90) REVERT: F 398 MET cc_start: 0.7384 (mmm) cc_final: 0.7148 (mmm) REVERT: F 548 GLN cc_start: 0.6629 (tp-100) cc_final: 0.6034 (tm-30) outliers start: 61 outliers final: 41 residues processed: 239 average time/residue: 0.3820 time to fit residues: 149.8742 Evaluate side-chains 220 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 618 ASN Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 209 optimal weight: 0.0770 chunk 311 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 368 optimal weight: 10.0000 chunk 230 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29270 Z= 0.220 Angle : 0.539 10.418 39710 Z= 0.269 Chirality : 0.042 0.175 4762 Planarity : 0.004 0.047 5094 Dihedral : 6.580 81.346 4285 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.51 % Allowed : 17.15 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3806 helix: 0.69 (0.14), residues: 1490 sheet: -2.24 (0.19), residues: 587 loop : -1.13 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 375 HIS 0.003 0.001 HIS C 93 PHE 0.019 0.001 PHE D 10 TYR 0.026 0.002 TYR F 531 ARG 0.005 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 182 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7716 (mpt-90) cc_final: 0.6773 (mmm160) REVERT: D 612 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8037 (pttp) REVERT: C 1 MET cc_start: 0.6824 (ptp) cc_final: 0.6380 (ppp) REVERT: C 92 VAL cc_start: 0.6143 (OUTLIER) cc_final: 0.5750 (p) REVERT: C 470 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8440 (mp) REVERT: C 476 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7961 (tttm) REVERT: C 488 VAL cc_start: 0.8666 (t) cc_final: 0.8375 (p) REVERT: A 1 MET cc_start: 0.7106 (ptp) cc_final: 0.6355 (pmm) REVERT: A 195 LEU cc_start: 0.8034 (mt) cc_final: 0.7640 (tp) REVERT: A 535 MET cc_start: 0.8889 (mtp) cc_final: 0.8670 (mtp) REVERT: A 591 MET cc_start: 0.7383 (tmm) cc_final: 0.7168 (tmm) REVERT: F 40 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6299 (ttp-170) REVERT: F 42 LEU cc_start: 0.6909 (tt) cc_final: 0.6679 (tp) REVERT: F 97 TYR cc_start: 0.8008 (p90) cc_final: 0.7431 (p90) REVERT: F 398 MET cc_start: 0.7439 (mmm) cc_final: 0.7125 (mmm) REVERT: F 410 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7192 (tp) REVERT: F 548 GLN cc_start: 0.6627 (tp-100) cc_final: 0.6265 (tm-30) outliers start: 72 outliers final: 53 residues processed: 244 average time/residue: 0.3888 time to fit residues: 156.8608 Evaluate side-chains 232 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 410 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 556 GLN E 618 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29270 Z= 0.180 Angle : 0.526 11.892 39710 Z= 0.263 Chirality : 0.042 0.248 4762 Planarity : 0.004 0.045 5094 Dihedral : 6.444 81.011 4285 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 2.33 % Allowed : 17.57 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3806 helix: 0.81 (0.14), residues: 1481 sheet: -2.15 (0.19), residues: 588 loop : -1.05 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 375 HIS 0.012 0.001 HIS F 249 PHE 0.017 0.001 PHE D 10 TYR 0.031 0.002 TYR F 531 ARG 0.012 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 180 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7724 (mpt-90) cc_final: 0.6707 (mmm160) REVERT: D 612 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8014 (pttp) REVERT: C 1 MET cc_start: 0.6795 (ptp) cc_final: 0.6407 (ppp) REVERT: C 92 VAL cc_start: 0.6392 (OUTLIER) cc_final: 0.5985 (p) REVERT: C 200 MET cc_start: 0.5693 (tpp) cc_final: 0.5482 (mmt) REVERT: C 470 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 476 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: C 488 VAL cc_start: 0.8661 (t) cc_final: 0.8364 (p) REVERT: A 1 MET cc_start: 0.7057 (ptp) cc_final: 0.6320 (pmm) REVERT: A 195 LEU cc_start: 0.8022 (mt) cc_final: 0.7618 (tp) REVERT: A 303 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7953 (tt) REVERT: A 535 MET cc_start: 0.8866 (mtp) cc_final: 0.8659 (mtp) REVERT: F 97 TYR cc_start: 0.7921 (p90) cc_final: 0.7389 (p90) REVERT: F 147 MET cc_start: 0.5407 (ptp) cc_final: 0.5110 (pmm) REVERT: F 398 MET cc_start: 0.7492 (mmm) cc_final: 0.7126 (mmm) REVERT: F 410 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7140 (tp) REVERT: F 548 GLN cc_start: 0.6615 (tp-100) cc_final: 0.6268 (tm-30) REVERT: F 591 MET cc_start: 0.8710 (tmm) cc_final: 0.8088 (tmm) outliers start: 67 outliers final: 55 residues processed: 239 average time/residue: 0.3717 time to fit residues: 146.4445 Evaluate side-chains 230 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 170 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 553 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 0.9990 chunk 352 optimal weight: 7.9990 chunk 321 optimal weight: 7.9990 chunk 343 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 310 optimal weight: 40.0000 chunk 324 optimal weight: 30.0000 chunk 341 optimal weight: 0.4980 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29270 Z= 0.222 Angle : 0.545 14.990 39710 Z= 0.271 Chirality : 0.042 0.204 4762 Planarity : 0.004 0.061 5094 Dihedral : 6.428 80.142 4285 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 2.44 % Allowed : 17.64 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3806 helix: 0.86 (0.14), residues: 1483 sheet: -2.14 (0.19), residues: 602 loop : -1.03 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 375 HIS 0.003 0.001 HIS F 249 PHE 0.016 0.001 PHE E 180 TYR 0.027 0.002 TYR F 341 ARG 0.015 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 180 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7731 (mpt-90) cc_final: 0.6723 (mmm160) REVERT: D 612 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8026 (pttp) REVERT: C 31 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7559 (mttt) REVERT: C 92 VAL cc_start: 0.6411 (OUTLIER) cc_final: 0.6009 (p) REVERT: C 470 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8403 (mp) REVERT: C 476 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7952 (tttm) REVERT: C 488 VAL cc_start: 0.8674 (t) cc_final: 0.8383 (p) REVERT: B 525 MET cc_start: 0.8342 (mtt) cc_final: 0.8088 (mtt) REVERT: A 1 MET cc_start: 0.7046 (ptp) cc_final: 0.6329 (pmm) REVERT: A 195 LEU cc_start: 0.8021 (mt) cc_final: 0.7616 (tp) REVERT: A 303 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7962 (tt) REVERT: A 535 MET cc_start: 0.8891 (mtp) cc_final: 0.8644 (mtp) REVERT: F 97 TYR cc_start: 0.7941 (p90) cc_final: 0.7562 (p90) REVERT: F 147 MET cc_start: 0.5433 (ptp) cc_final: 0.5100 (pmm) REVERT: F 398 MET cc_start: 0.7408 (mmm) cc_final: 0.7073 (mmm) REVERT: F 410 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7153 (tp) REVERT: F 548 GLN cc_start: 0.6688 (tp-100) cc_final: 0.6363 (tm-30) outliers start: 70 outliers final: 59 residues processed: 240 average time/residue: 0.3899 time to fit residues: 154.4611 Evaluate side-chains 240 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 175 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 553 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 0.7980 chunk 362 optimal weight: 0.5980 chunk 221 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 chunk 380 optimal weight: 0.3980 chunk 350 optimal weight: 1.9990 chunk 303 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN B 344 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29270 Z= 0.166 Angle : 0.541 14.047 39710 Z= 0.267 Chirality : 0.042 0.202 4762 Planarity : 0.004 0.088 5094 Dihedral : 6.282 79.725 4285 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 2.16 % Allowed : 17.92 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3806 helix: 0.88 (0.14), residues: 1484 sheet: -2.04 (0.19), residues: 614 loop : -0.96 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 375 HIS 0.004 0.000 HIS F 249 PHE 0.013 0.001 PHE B 186 TYR 0.025 0.002 TYR B 341 ARG 0.016 0.000 ARG F 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7612 Ramachandran restraints generated. 3806 Oldfield, 0 Emsley, 3806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 182 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7731 (mpt-90) cc_final: 0.6570 (mmm160) REVERT: D 612 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8014 (pttp) REVERT: C 31 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7541 (mttt) REVERT: C 92 VAL cc_start: 0.6328 (OUTLIER) cc_final: 0.5915 (p) REVERT: C 119 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8808 (m) REVERT: C 470 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8126 (mp) REVERT: C 488 VAL cc_start: 0.8672 (t) cc_final: 0.8379 (p) REVERT: B 525 MET cc_start: 0.8391 (mtt) cc_final: 0.8130 (mtt) REVERT: A 1 MET cc_start: 0.7016 (ptp) cc_final: 0.6312 (pmm) REVERT: A 195 LEU cc_start: 0.8006 (mt) cc_final: 0.7575 (tp) REVERT: A 303 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7947 (tt) REVERT: F 97 TYR cc_start: 0.7832 (p90) cc_final: 0.7575 (p90) REVERT: F 147 MET cc_start: 0.5403 (ptp) cc_final: 0.5098 (pmm) REVERT: F 398 MET cc_start: 0.7420 (mmm) cc_final: 0.7091 (mmm) REVERT: F 410 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7096 (tp) REVERT: F 548 GLN cc_start: 0.6637 (tp-100) cc_final: 0.6333 (tm-30) REVERT: F 591 MET cc_start: 0.8700 (tmm) cc_final: 0.8076 (tmm) outliers start: 62 outliers final: 53 residues processed: 236 average time/residue: 0.3757 time to fit residues: 146.9941 Evaluate side-chains 233 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 174 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 575 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 553 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 0.8980 chunk 322 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 279 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 127 optimal weight: 0.0670 chunk 311 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 HIS ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN B 344 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.133632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.104514 restraints weight = 76452.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.102878 restraints weight = 58449.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.103773 restraints weight = 61900.818| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29270 Z= 0.156 Angle : 0.536 13.858 39710 Z= 0.266 Chirality : 0.042 0.199 4762 Planarity : 0.004 0.046 5094 Dihedral : 6.162 78.843 4285 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.23 % Allowed : 18.34 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3806 helix: 0.92 (0.14), residues: 1482 sheet: -1.96 (0.19), residues: 604 loop : -0.94 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 375 HIS 0.005 0.001 HIS F 249 PHE 0.014 0.001 PHE B 186 TYR 0.030 0.002 TYR F 341 ARG 0.013 0.000 ARG C 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5435.23 seconds wall clock time: 98 minutes 41.39 seconds (5921.39 seconds total)