Starting phenix.real_space_refine on Tue May 14 21:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/05_2024/8x7u_38111_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/05_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_38111/05_2024/8x7u_38111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/05_2024/8x7u_38111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/05_2024/8x7u_38111_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7u_38111/05_2024/8x7u_38111_updated.pdb" } 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 15.99, per 1000 atoms: 0.55 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: 11.28 Conformation dependent library (CDL) restraints added in 5.1 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... running ksdssp... Secondary structure from input PDB file: 142 helices and 47 sheets defined 35.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 28 through 35 Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 65 through 80 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 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 295 through 305 Processing helix chain 'D' and resid 335 through 345 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 381 through 384 No H-bonds generated for 'chain 'D' and resid 381 through 384' Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.735A pdb=" N GLU D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 457 through 460 No H-bonds generated for 'chain 'D' and resid 457 through 460' Processing helix chain 'D' and resid 475 through 490 Processing helix chain 'D' and resid 502 through 515 Processing helix chain 'D' and resid 522 through 535 Processing helix chain 'D' and resid 554 through 570 Processing helix chain 'D' and resid 578 through 595 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 641 through 650 Processing helix chain 'D' and resid 655 through 668 Processing helix chain 'C' and resid 3 through 13 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 35 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 46 through 52 removed outlier: 3.505A pdb=" N PHE C 52 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 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 64 through 79 removed outlier: 3.551A pdb=" N LEU C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 264 through 275 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 279 through 286 Processing helix chain 'C' and resid 295 through 305 Processing helix chain 'C' and resid 335 through 345 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 381 through 384 No H-bonds generated for 'chain 'C' and resid 381 through 384' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 449 through 452 No H-bonds generated for 'chain 'C' and resid 449 through 452' Processing helix chain 'C' and resid 457 through 460 No H-bonds generated for 'chain 'C' and resid 457 through 460' Processing helix chain 'C' and resid 475 through 490 Processing helix chain 'C' and resid 493 through 496 No H-bonds generated for 'chain 'C' and resid 493 through 496' Processing helix chain 'C' and resid 502 through 515 removed outlier: 3.922A pdb=" N LYS C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 537 Processing helix chain 'C' and resid 554 through 570 Processing helix chain 'C' and resid 578 through 595 Processing helix chain 'C' and resid 604 through 607 No H-bonds generated for 'chain 'C' and resid 604 through 607' Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 641 through 644 No H-bonds generated for 'chain 'C' and resid 641 through 644' Processing helix chain 'C' and resid 646 through 649 No H-bonds generated for 'chain 'C' and resid 646 through 649' Processing helix chain 'C' and resid 655 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 3 through 13 Processing helix chain 'B' and resid 28 through 35 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 46 through 52 Processing helix chain 'B' and resid 54 through 62 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 64 through 80 removed outlier: 3.904A pdb=" N ALA B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 195 through 198 removed outlier: 3.658A pdb=" N GLY B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 264 through 275 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 279 through 286 Processing helix chain 'B' and resid 295 through 305 Processing helix chain 'B' and resid 335 through 345 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 381 through 384 No H-bonds generated for 'chain 'B' and resid 381 through 384' Processing helix chain 'B' and resid 400 through 409 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 449 through 452 No H-bonds generated for 'chain 'B' and resid 449 through 452' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 475 through 490 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.532A pdb=" N LYS B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 535 Processing helix chain 'B' and resid 554 through 570 Processing helix chain 'B' and resid 578 through 594 removed outlier: 3.527A pdb=" N THR B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 621 removed outlier: 3.611A pdb=" N ILE B 620 " --> pdb=" O LYS B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 649 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 657 through 667 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) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 28 through 35 removed outlier: 3.864A pdb=" N ASP E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 52 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 54 through 62 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 64 through 80 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) Processing helix chain 'E' and resid 192 through 195 No H-bonds generated for 'chain 'E' and resid 192 through 195' Processing helix chain 'E' and resid 264 through 275 Processing helix chain 'E' and resid 279 through 286 Processing helix chain 'E' and resid 295 through 305 Processing helix chain 'E' and resid 335 through 345 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 381 through 384 No H-bonds generated for 'chain 'E' and resid 381 through 384' Processing helix chain 'E' and resid 395 through 397 No H-bonds generated for 'chain 'E' and resid 395 through 397' Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 406 through 411 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) No H-bonds generated for 'chain 'E' and resid 406 through 411' Processing helix chain 'E' and resid 457 through 460 No H-bonds generated for 'chain 'E' and resid 457 through 460' Processing helix chain 'E' and resid 475 through 490 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 493 through 496 No H-bonds generated for 'chain 'E' and resid 493 through 496' Processing helix chain 'E' and resid 502 through 512 removed outlier: 3.813A pdb=" N LYS E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 540 through 542 No H-bonds generated for 'chain 'E' and resid 540 through 542' Processing helix chain 'E' and resid 554 through 570 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) Processing helix chain 'E' and resid 578 through 595 Processing helix chain 'E' and resid 615 through 621 Processing helix chain 'E' and resid 640 through 650 removed outlier: 3.727A pdb=" N GLU E 645 " --> pdb=" O GLU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 668 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 3 through 13 Processing helix chain 'A' and resid 28 through 35 removed outlier: 3.880A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 54 through 62 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 64 through 80 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 279 through 286 removed outlier: 4.339A pdb=" N VAL A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.609A pdb=" N ALA A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 400 through 410 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 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 449 through 452 No H-bonds generated for 'chain 'A' and resid 449 through 452' Processing helix chain 'A' and resid 457 through 462 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) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.563A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 533 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 554 through 570 removed outlier: 3.548A pdb=" N ALA A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 594 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 3 through 12 Processing helix chain 'F' and resid 28 through 35 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 46 through 52 removed outlier: 3.576A pdb=" N SER F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 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 64 through 80 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 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 255 through 258 No H-bonds generated for 'chain 'F' and resid 255 through 258' Processing helix chain 'F' and resid 264 through 275 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 279 through 286 removed outlier: 3.660A pdb=" N VAL F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 305 Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 338 through 345 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 381 through 384 No H-bonds generated for 'chain 'F' and resid 381 through 384' Processing helix chain 'F' and resid 400 through 409 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 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 457 through 462 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) No H-bonds generated for 'chain 'F' and resid 457 through 462' Processing helix chain 'F' and resid 475 through 490 removed outlier: 3.599A pdb=" N ILE F 485 " --> pdb=" O ILE F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 496 No H-bonds generated for 'chain 'F' and resid 493 through 496' Processing helix chain 'F' and resid 502 through 514 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 522 through 536 Processing helix chain 'F' and resid 554 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 578 through 595 Processing helix chain 'F' and resid 604 through 606 No H-bonds generated for 'chain 'F' and resid 604 through 606' Processing helix chain 'F' and resid 615 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 649 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 657 through 666 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= A, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= B, first strand: chain 'D' and resid 221 through 224 removed outlier: 6.551A pdb=" N ARG D 187 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL D 126 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER D 185 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.992A pdb=" N ARG D 179 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 138 through 140 Processing sheet with id= E, first strand: chain 'D' and resid 325 through 329 removed outlier: 6.712A pdb=" N LEU D 465 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL D 328 " --> pdb=" O LEU D 465 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE D 467 " --> pdb=" O VAL D 328 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 365 through 368 Processing sheet with id= G, first strand: chain 'D' and resid 388 through 390 Processing sheet with id= H, first strand: chain 'D' and resid 414 through 417 Processing sheet with id= I, first strand: chain 'D' and resid 225 through 231 removed outlier: 6.097A pdb=" N VAL D 227 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL D 247 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG D 229 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU D 245 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE D 231 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS D 243 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.461A pdb=" N HIS C 93 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 44 " --> pdb=" O HIS C 93 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG C 95 " --> pdb=" O ILE C 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.610A pdb=" N ARG C 187 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 126 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER C 185 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 148 through 150 removed outlier: 7.263A pdb=" N ARG C 179 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 138 through 140 Processing sheet with id= N, first strand: chain 'C' and resid 325 through 329 removed outlier: 6.652A pdb=" N LEU C 465 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 328 " --> pdb=" O LEU C 465 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE C 467 " --> pdb=" O VAL C 328 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 365 through 368 Processing sheet with id= P, 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= Q, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.433A pdb=" N HIS B 93 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 44 " --> pdb=" O HIS B 93 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG B 95 " --> pdb=" O ILE B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'B' and resid 220 through 224 removed outlier: 3.864A pdb=" N ASP B 220 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 187 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 126 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER B 185 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 227 through 231 removed outlier: 3.839A pdb=" N LYS B 242 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.729A pdb=" N LEU B 465 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 328 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE B 467 " --> pdb=" O VAL B 328 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'B' and resid 365 through 368 Processing sheet with id= V, first strand: chain 'B' and resid 388 through 390 Processing sheet with id= W, first strand: chain 'B' and resid 414 through 419 Processing sheet with id= X, 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= Y, first strand: chain 'E' and resid 43 through 45 removed outlier: 6.262A pdb=" N ARG E 95 " --> pdb=" O ILE E 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 221 through 224 removed outlier: 6.489A pdb=" N ARG E 187 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL E 126 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER E 185 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 138 through 140 Processing sheet with id= AB, first strand: chain 'E' and resid 227 through 230 Processing sheet with id= AC, 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: 6.750A pdb=" N LEU E 465 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL E 328 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N PHE E 467 " --> pdb=" O VAL E 328 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'E' and resid 365 through 368 Processing sheet with id= AE, first strand: chain 'E' and resid 414 through 417 Processing sheet with id= AF, first strand: chain 'E' and resid 130 through 135 removed outlier: 6.507A pdb=" N ARG E 179 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.690A pdb=" N HIS A 93 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 44 " --> pdb=" O HIS A 93 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG A 95 " --> pdb=" O ILE A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'A' and resid 116 through 121 removed outlier: 6.113A pdb=" N VAL A 227 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A 247 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.830A pdb=" N ARG A 125 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN A 189 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE A 123 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.338A pdb=" N LEU A 465 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 328 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE A 467 " --> pdb=" O VAL A 328 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.706A pdb=" N PHE A 389 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 352 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU A 391 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 435 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id= AL, 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= AM, first strand: chain 'A' and resid 414 through 417 Processing sheet with id= AN, 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) Processing sheet with id= AO, first strand: chain 'F' and resid 102 through 104 removed outlier: 8.590A pdb=" N LEU F 103 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN F 118 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL F 227 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL F 247 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 148 through 150 removed outlier: 7.187A pdb=" N ARG F 179 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'F' and resid 138 through 140 Processing sheet with id= AR, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.568A pdb=" N GLN F 184 " --> pdb=" O LEU F 208 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 125 " --> pdb=" O ARG F 187 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLN F 189 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE F 123 " --> pdb=" O GLN F 189 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 465 through 469 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) Processing sheet with id= AT, 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= AU, 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) 886 hydrogen bonds defined for protein. 2574 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: 11.22 Time building geometry restraints manager: 12.23 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: 295 2.62 - 3.19: 26088 3.19 - 3.76: 45890 3.76 - 4.33: 63742 4.33 - 4.90: 100868 Nonbonded interactions: 236883 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 GLY F 380 " pdb=" N LEU F 384 " model vdw 2.267 2.520 nonbonded pdb=" O VAL F 610 " pdb=" OG SER F 614 " model vdw 2.273 2.440 ... (remaining 236878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.780 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 78.530 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.000 ------------------------------------------------------------------------------- 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= 0.197 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 : 3.375 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: 0.5481 time to fit residues: 345.2416 Evaluate side-chains 240 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 3.392 ------------------------------------------------------------------------------- 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: 7.9990 chunk 289 optimal weight: 20.0000 chunk 160 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 0.2980 chunk 222 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 overall best weight: 2.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** 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 E 98 ASN E 151 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN E 413 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 344 ASN F 412 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29270 Z= 0.347 Angle : 0.610 9.945 39710 Z= 0.306 Chirality : 0.043 0.190 4762 Planarity : 0.004 0.046 5094 Dihedral : 7.186 84.770 4295 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.88 % Allowed : 10.79 % Favored : 87.33 % 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: -2.37 (0.12), residues: 3806 helix: -0.86 (0.13), residues: 1443 sheet: -2.69 (0.17), residues: 659 loop : -1.59 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 46 HIS 0.006 0.001 HIS D 294 PHE 0.017 0.002 PHE E 183 TYR 0.024 0.002 TYR B 531 ARG 0.010 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 291 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.7713 (ttmm) cc_final: 0.7485 (ttmm) REVERT: D 152 ARG cc_start: 0.7457 (mpt-90) cc_final: 0.6496 (mmm160) REVERT: D 202 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6083 (mpp80) REVERT: D 240 ILE cc_start: 0.6639 (pt) cc_final: 0.6388 (pt) REVERT: D 241 PHE cc_start: 0.6795 (m-80) cc_final: 0.6457 (m-80) REVERT: D 246 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7430 (tm-30) REVERT: D 355 LYS cc_start: 0.7576 (mmtm) cc_final: 0.7314 (mmtp) REVERT: D 483 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7481 (tm-30) REVERT: D 612 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8007 (pttp) REVERT: C 446 HIS cc_start: 0.7818 (m-70) cc_final: 0.7582 (m-70) REVERT: C 481 ILE cc_start: 0.8843 (tt) cc_final: 0.8450 (pt) REVERT: B 10 PHE cc_start: 0.7654 (m-80) cc_final: 0.7417 (m-80) REVERT: B 525 MET cc_start: 0.8235 (mtp) cc_final: 0.7993 (mtp) REVERT: E 200 MET cc_start: 0.2413 (mmp) cc_final: 0.1571 (ptt) REVERT: E 580 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: A 1 MET cc_start: 0.7095 (ptp) cc_final: 0.6449 (pmm) REVERT: F 42 LEU cc_start: 0.7294 (tt) cc_final: 0.6792 (tp) REVERT: F 103 LEU cc_start: 0.7771 (tp) cc_final: 0.7501 (tp) REVERT: F 303 LEU cc_start: 0.8100 (mt) cc_final: 0.7847 (mp) REVERT: F 398 MET cc_start: 0.7281 (mmm) cc_final: 0.6989 (mmm) REVERT: F 548 GLN cc_start: 0.6518 (tp-100) cc_final: 0.6092 (tm-30) REVERT: F 591 MET cc_start: 0.8726 (tmm) cc_final: 0.7787 (tmm) REVERT: F 592 MET cc_start: 0.7659 (mmm) cc_final: 0.7374 (mmm) outliers start: 54 outliers final: 29 residues processed: 282 average time/residue: 0.4389 time to fit residues: 195.5558 Evaluate side-chains 230 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain C residue 106 LYS 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 244 ILE Chi-restraints excluded: chain E residue 291 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 E residue 580 ASP Chi-restraints excluded: chain A residue 36 VAL 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 36 VAL Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 347 optimal weight: 7.9990 chunk 375 optimal weight: 0.3980 chunk 309 optimal weight: 0.9990 chunk 344 optimal weight: 20.0000 chunk 118 optimal weight: 0.4980 chunk 278 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN D 437 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 GLN ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN E 189 GLN E 413 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** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29270 Z= 0.238 Angle : 0.536 10.362 39710 Z= 0.266 Chirality : 0.042 0.173 4762 Planarity : 0.004 0.042 5094 Dihedral : 6.937 88.619 4291 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 2.12 % Allowed : 13.19 % Favored : 84.69 % 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: -1.62 (0.13), residues: 3806 helix: -0.02 (0.14), residues: 1434 sheet: -2.47 (0.18), residues: 620 loop : -1.34 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 46 HIS 0.006 0.001 HIS A 407 PHE 0.016 0.001 PHE C 10 TYR 0.025 0.002 TYR B 531 ARG 0.011 0.000 ARG F 95 *********************** 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 274 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 213 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7546 (mpt-90) cc_final: 0.6558 (mmm160) REVERT: D 202 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6214 (mpp80) REVERT: D 241 PHE cc_start: 0.6860 (m-80) cc_final: 0.6300 (m-80) REVERT: D 246 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7465 (tm-30) REVERT: D 355 LYS cc_start: 0.7581 (mmtm) cc_final: 0.7359 (mmtp) REVERT: D 612 LYS cc_start: 0.8614 (ttmt) cc_final: 0.7956 (pttp) REVERT: C 189 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: C 446 HIS cc_start: 0.7874 (m-70) cc_final: 0.7628 (m-70) REVERT: C 470 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 481 ILE cc_start: 0.8844 (tt) cc_final: 0.8610 (mt) REVERT: C 488 VAL cc_start: 0.8822 (t) cc_final: 0.8487 (p) REVERT: C 603 LEU cc_start: 0.5466 (mt) cc_final: 0.5203 (pt) REVERT: B 446 HIS cc_start: 0.8052 (m-70) cc_final: 0.7851 (m90) REVERT: E 580 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: A 1 MET cc_start: 0.7144 (ptp) cc_final: 0.6504 (pmm) REVERT: A 195 LEU cc_start: 0.7954 (mt) cc_final: 0.7436 (tp) REVERT: F 42 LEU cc_start: 0.7214 (tt) cc_final: 0.6786 (tp) REVERT: F 200 MET cc_start: 0.3847 (tpt) cc_final: 0.2898 (ttt) REVERT: F 398 MET cc_start: 0.7438 (mmm) cc_final: 0.6738 (mmm) REVERT: F 548 GLN cc_start: 0.6534 (tp-100) cc_final: 0.5960 (tm-30) REVERT: F 591 MET cc_start: 0.8763 (tmm) cc_final: 0.7921 (tmm) REVERT: F 592 MET cc_start: 0.7675 (mmm) cc_final: 0.7378 (mmm) outliers start: 61 outliers final: 31 residues processed: 264 average time/residue: 0.4344 time to fit residues: 182.0137 Evaluate side-chains 224 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 ASN 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 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 330 ASP 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 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 128 GLU 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 E residue 580 ASP Chi-restraints excluded: chain A residue 36 VAL 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 36 VAL Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 348 optimal weight: 30.0000 chunk 369 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 330 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 413 GLN B 515 ASN ** 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 444 ASN F 446 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 29270 Z= 0.521 Angle : 0.704 9.496 39710 Z= 0.350 Chirality : 0.046 0.244 4762 Planarity : 0.005 0.056 5094 Dihedral : 7.209 81.680 4289 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 3.20 % Allowed : 15.31 % Favored : 81.49 % 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: -1.62 (0.13), residues: 3806 helix: 0.00 (0.14), residues: 1458 sheet: -2.37 (0.19), residues: 572 loop : -1.46 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 375 HIS 0.009 0.002 HIS D 484 PHE 0.024 0.002 PHE E 183 TYR 0.023 0.003 TYR E 154 ARG 0.027 0.001 ARG A 311 *********************** 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 287 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 195 time to evaluate : 3.112 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 6 MET cc_start: 0.8288 (mtp) cc_final: 0.7970 (mtt) REVERT: D 63 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7404 (p0) REVERT: D 152 ARG cc_start: 0.7667 (mpt-90) cc_final: 0.6739 (mmm160) REVERT: D 241 PHE cc_start: 0.6875 (m-80) cc_final: 0.6525 (m-80) REVERT: D 612 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8053 (pttp) REVERT: C 481 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8467 (pt) REVERT: B 446 HIS cc_start: 0.8171 (m-70) cc_final: 0.7956 (m90) REVERT: B 531 TYR cc_start: 0.8710 (t80) cc_final: 0.8467 (t80) REVERT: A 1 MET cc_start: 0.7146 (ptp) cc_final: 0.6522 (pmm) REVERT: A 195 LEU cc_start: 0.7996 (mt) cc_final: 0.7535 (tp) REVERT: F 42 LEU cc_start: 0.7152 (tt) cc_final: 0.6770 (tp) REVERT: F 412 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: F 591 MET cc_start: 0.8788 (tmm) cc_final: 0.7856 (tmm) REVERT: F 592 MET cc_start: 0.7787 (mmm) cc_final: 0.7430 (mmm) outliers start: 92 outliers final: 60 residues processed: 272 average time/residue: 0.4017 time to fit residues: 178.4274 Evaluate side-chains 241 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 178 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 367 VAL 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 119 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 147 MET 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 481 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain B residue 36 VAL 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 570 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 132 PHE Chi-restraints excluded: chain E residue 133 VAL 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 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 36 VAL 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 36 VAL 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 309 VAL Chi-restraints excluded: chain F residue 412 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 274 optimal weight: 30.0000 chunk 152 optimal weight: 4.9990 chunk 315 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 188 optimal weight: 0.5980 chunk 331 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 427 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN F 62 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29270 Z= 0.319 Angle : 0.578 9.561 39710 Z= 0.287 Chirality : 0.043 0.184 4762 Planarity : 0.004 0.042 5094 Dihedral : 6.977 80.367 4289 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 3.20 % Allowed : 16.67 % Favored : 80.13 % 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: 0.23 (0.14), residues: 1457 sheet: -2.32 (0.19), residues: 581 loop : -1.34 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 46 HIS 0.005 0.001 HIS C 93 PHE 0.019 0.002 PHE D 306 TYR 0.016 0.002 TYR F 531 ARG 0.005 0.000 ARG D 462 *********************** 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 278 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 186 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 MET cc_start: 0.8322 (mtp) cc_final: 0.8058 (mtt) REVERT: D 135 LYS cc_start: 0.8045 (mttp) cc_final: 0.7780 (mptt) REVERT: D 152 ARG cc_start: 0.7665 (mpt-90) cc_final: 0.6685 (mmm160) REVERT: D 202 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6400 (mpt-90) REVERT: D 612 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8036 (pttp) REVERT: C 470 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8471 (mp) REVERT: C 481 ILE cc_start: 0.8905 (tt) cc_final: 0.8512 (mt) REVERT: C 488 VAL cc_start: 0.8784 (t) cc_final: 0.8464 (p) REVERT: B 425 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8243 (p) REVERT: B 446 HIS cc_start: 0.8154 (m-70) cc_final: 0.7919 (m90) REVERT: B 531 TYR cc_start: 0.8759 (t80) cc_final: 0.8339 (t80) REVERT: B 532 TYR cc_start: 0.8588 (t80) cc_final: 0.8302 (t80) REVERT: B 535 MET cc_start: 0.8420 (mmm) cc_final: 0.8219 (mmm) REVERT: A 1 MET cc_start: 0.7033 (ptp) cc_final: 0.6415 (pmm) REVERT: A 195 LEU cc_start: 0.8005 (mt) cc_final: 0.7582 (tp) REVERT: F 42 LEU cc_start: 0.7068 (tt) cc_final: 0.6690 (tp) REVERT: F 200 MET cc_start: 0.4696 (tpt) cc_final: 0.3550 (ttt) REVERT: F 246 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5018 (tp30) REVERT: F 398 MET cc_start: 0.7483 (mmm) cc_final: 0.7234 (mmm) REVERT: F 412 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: F 548 GLN cc_start: 0.6704 (tp-100) cc_final: 0.6173 (tm-30) REVERT: F 591 MET cc_start: 0.8779 (tmm) cc_final: 0.7949 (tmm) REVERT: F 592 MET cc_start: 0.7792 (mmm) cc_final: 0.7532 (mmm) outliers start: 92 outliers final: 60 residues processed: 260 average time/residue: 0.3899 time to fit residues: 167.3642 Evaluate side-chains 245 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 180 time to evaluate : 3.321 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 GLU 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 139 VAL Chi-restraints excluded: chain C residue 147 MET 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 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 425 THR Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 570 MET 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 132 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 225 THR 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 382 LEU 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 36 VAL 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 36 VAL Chi-restraints excluded: chain F residue 48 HIS 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 246 GLU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 412 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 0.0060 chunk 332 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 369 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 122 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3657 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= 0.148 Angle : 0.507 8.345 39710 Z= 0.253 Chirality : 0.041 0.178 4762 Planarity : 0.004 0.084 5094 Dihedral : 6.626 80.352 4289 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 2.47 % Allowed : 18.02 % Favored : 79.51 % 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 (0.13), residues: 3806 helix: 0.55 (0.14), residues: 1460 sheet: -2.14 (0.20), residues: 572 loop : -1.14 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 375 HIS 0.003 0.001 HIS A 567 PHE 0.020 0.001 PHE C 10 TYR 0.027 0.001 TYR F 341 ARG 0.005 0.000 ARG F 271 *********************** 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 266 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 195 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7749 (mpt-90) cc_final: 0.6814 (mmm160) REVERT: D 202 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6384 (mpt-90) REVERT: D 240 ILE cc_start: 0.6064 (pt) cc_final: 0.5782 (pt) REVERT: D 612 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8037 (pttp) REVERT: C 92 VAL cc_start: 0.6146 (OUTLIER) cc_final: 0.5757 (p) REVERT: C 200 MET cc_start: 0.5811 (tpp) cc_final: 0.5569 (mmt) REVERT: C 470 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 481 ILE cc_start: 0.8860 (tt) cc_final: 0.8563 (mt) REVERT: C 488 VAL cc_start: 0.8729 (t) cc_final: 0.8402 (p) REVERT: B 425 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 430 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.9001 (m) REVERT: B 446 HIS cc_start: 0.8121 (m-70) cc_final: 0.7908 (m90) REVERT: B 531 TYR cc_start: 0.8769 (t80) cc_final: 0.8364 (t80) REVERT: B 532 TYR cc_start: 0.8548 (t80) cc_final: 0.8247 (t80) REVERT: B 535 MET cc_start: 0.8340 (mmm) cc_final: 0.8133 (mmm) REVERT: E 580 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: A 1 MET cc_start: 0.7270 (ptp) cc_final: 0.6626 (pmm) REVERT: A 195 LEU cc_start: 0.8012 (mt) cc_final: 0.7601 (tp) REVERT: F 42 LEU cc_start: 0.6980 (tt) cc_final: 0.6633 (tp) REVERT: F 142 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.5750 (t0) REVERT: F 200 MET cc_start: 0.4726 (tpt) cc_final: 0.3580 (ttt) REVERT: F 398 MET cc_start: 0.7666 (mmm) cc_final: 0.7184 (mmm) REVERT: F 548 GLN cc_start: 0.6568 (tp-100) cc_final: 0.5991 (tm-30) REVERT: F 591 MET cc_start: 0.8730 (tmm) cc_final: 0.7900 (tmm) REVERT: F 592 MET cc_start: 0.7851 (mmm) cc_final: 0.7506 (mmm) outliers start: 71 outliers final: 46 residues processed: 255 average time/residue: 0.3909 time to fit residues: 164.1355 Evaluate side-chains 233 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 315 ASP 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 56 LEU 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 145 ASN Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 330 ASP 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 425 THR Chi-restraints excluded: chain B residue 430 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 68 ILE 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 309 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 36 VAL 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 363 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 224 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: 0.8980 chunk 210 optimal weight: 0.7980 chunk 269 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 311 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 368 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN E 118 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: 0.7492 moved from start: 0.3865 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= 0.234 Angle : 0.534 8.163 39710 Z= 0.264 Chirality : 0.042 0.242 4762 Planarity : 0.004 0.043 5094 Dihedral : 6.597 75.412 4289 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 2.64 % Allowed : 18.30 % Favored : 79.05 % 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: -0.93 (0.14), residues: 3806 helix: 0.66 (0.14), residues: 1456 sheet: -2.06 (0.20), residues: 594 loop : -1.11 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 46 HIS 0.004 0.001 HIS B 294 PHE 0.017 0.001 PHE D 10 TYR 0.021 0.002 TYR F 531 ARG 0.016 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 259 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 183 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7769 (mpt-90) cc_final: 0.6805 (mmm160) REVERT: D 202 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6348 (mpt-90) REVERT: D 240 ILE cc_start: 0.6277 (pt) cc_final: 0.5942 (pt) REVERT: D 612 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8022 (pttp) REVERT: C 92 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6023 (p) REVERT: C 200 MET cc_start: 0.5788 (tpp) cc_final: 0.5554 (mmt) REVERT: C 470 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8376 (mp) REVERT: C 481 ILE cc_start: 0.8901 (tt) cc_final: 0.8537 (mt) REVERT: C 488 VAL cc_start: 0.8796 (t) cc_final: 0.8487 (p) REVERT: B 425 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8229 (p) REVERT: B 446 HIS cc_start: 0.8121 (m-70) cc_final: 0.7908 (m90) REVERT: B 531 TYR cc_start: 0.8836 (t80) cc_final: 0.8389 (t80) REVERT: B 535 MET cc_start: 0.8252 (mmm) cc_final: 0.8040 (mmm) REVERT: A 1 MET cc_start: 0.6905 (ptp) cc_final: 0.6195 (pmm) REVERT: A 195 LEU cc_start: 0.8003 (mt) cc_final: 0.7600 (tp) REVERT: F 42 LEU cc_start: 0.6981 (tt) cc_final: 0.6666 (tp) REVERT: F 147 MET cc_start: 0.5597 (ptp) cc_final: 0.5320 (pmm) REVERT: F 548 GLN cc_start: 0.6673 (tp-100) cc_final: 0.6215 (tm-30) REVERT: F 591 MET cc_start: 0.8760 (tmm) cc_final: 0.7964 (tmm) REVERT: F 592 MET cc_start: 0.7873 (mmm) cc_final: 0.7494 (mmm) outliers start: 76 outliers final: 59 residues processed: 245 average time/residue: 0.3711 time to fit residues: 151.7920 Evaluate side-chains 242 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 179 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 126 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 315 ASP Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 367 VAL 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 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 183 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 330 ASP 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 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 422 ILE 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 119 VAL Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 225 THR 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 382 LEU 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 36 VAL 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 363 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 36 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 234 optimal weight: 0.0170 chunk 250 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN B 344 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29270 Z= 0.167 Angle : 0.514 10.636 39710 Z= 0.253 Chirality : 0.041 0.210 4762 Planarity : 0.003 0.042 5094 Dihedral : 6.427 75.242 4289 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 2.54 % Allowed : 18.55 % Favored : 78.91 % 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: -0.78 (0.14), residues: 3806 helix: 0.80 (0.14), residues: 1449 sheet: -1.99 (0.20), residues: 592 loop : -1.04 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 375 HIS 0.002 0.001 HIS A 567 PHE 0.015 0.001 PHE B 186 TYR 0.025 0.001 TYR F 531 ARG 0.007 0.000 ARG F 578 *********************** 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 255 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 182 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7772 (mpt-90) cc_final: 0.6777 (mmm160) REVERT: D 202 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6192 (mpt-90) REVERT: D 240 ILE cc_start: 0.6234 (pt) cc_final: 0.5907 (pt) REVERT: D 612 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8032 (pttp) REVERT: C 92 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.5955 (p) REVERT: C 200 MET cc_start: 0.5753 (tpp) cc_final: 0.5517 (mmt) REVERT: C 470 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 481 ILE cc_start: 0.8860 (tt) cc_final: 0.8549 (mt) REVERT: C 488 VAL cc_start: 0.8766 (t) cc_final: 0.8452 (p) REVERT: B 248 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6939 (t0) REVERT: B 446 HIS cc_start: 0.8115 (m-70) cc_final: 0.7912 (m90) REVERT: B 531 TYR cc_start: 0.8825 (t80) cc_final: 0.8378 (t80) REVERT: E 580 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: A 1 MET cc_start: 0.6835 (ptp) cc_final: 0.6174 (pmm) REVERT: A 195 LEU cc_start: 0.8054 (mt) cc_final: 0.7647 (tp) REVERT: A 591 MET cc_start: 0.7403 (tmm) cc_final: 0.6707 (tmm) REVERT: F 42 LEU cc_start: 0.6989 (tt) cc_final: 0.6696 (tp) REVERT: F 97 TYR cc_start: 0.7789 (p90) cc_final: 0.7281 (p90) REVERT: F 147 MET cc_start: 0.5633 (ptp) cc_final: 0.5365 (pmm) REVERT: F 548 GLN cc_start: 0.6616 (tp-100) cc_final: 0.6173 (tm-30) REVERT: F 591 MET cc_start: 0.8752 (tmm) cc_final: 0.7931 (tmm) REVERT: F 592 MET cc_start: 0.7868 (mmm) cc_final: 0.7498 (mmm) outliers start: 73 outliers final: 56 residues processed: 243 average time/residue: 0.3825 time to fit residues: 154.4269 Evaluate side-chains 236 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 175 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 126 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 315 ASP 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 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 147 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain B residue 36 VAL 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 248 ASN Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 367 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 42 LEU Chi-restraints excluded: chain E residue 68 ILE 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 225 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain A residue 36 VAL 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 363 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 36 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 7.9990 chunk 352 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 343 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 324 optimal weight: 0.5980 chunk 341 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** B 248 ASN ** 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: 0.7469 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29270 Z= 0.180 Angle : 0.518 10.519 39710 Z= 0.255 Chirality : 0.041 0.206 4762 Planarity : 0.003 0.043 5094 Dihedral : 6.368 73.618 4289 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.53 % Rotamer: Outliers : 2.30 % Allowed : 19.00 % Favored : 78.71 % 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: -0.72 (0.14), residues: 3806 helix: 0.85 (0.14), residues: 1446 sheet: -1.95 (0.20), residues: 594 loop : -1.00 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 46 HIS 0.009 0.001 HIS B 249 PHE 0.014 0.001 PHE B 186 TYR 0.030 0.001 TYR F 531 ARG 0.007 0.000 ARG A 522 *********************** 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 246 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 180 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 ARG cc_start: 0.7795 (mpt-90) cc_final: 0.6778 (mmm160) REVERT: D 240 ILE cc_start: 0.6229 (pt) cc_final: 0.5900 (pt) REVERT: D 612 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8031 (pttp) REVERT: C 92 VAL cc_start: 0.6356 (OUTLIER) cc_final: 0.5966 (p) REVERT: C 200 MET cc_start: 0.5957 (tpp) cc_final: 0.5744 (mmt) REVERT: C 470 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 481 ILE cc_start: 0.8869 (tt) cc_final: 0.8548 (mt) REVERT: C 488 VAL cc_start: 0.8775 (t) cc_final: 0.8464 (p) REVERT: B 531 TYR cc_start: 0.8815 (t80) cc_final: 0.8555 (t80) REVERT: A 1 MET cc_start: 0.7027 (ptp) cc_final: 0.6332 (pmm) REVERT: A 195 LEU cc_start: 0.8040 (mt) cc_final: 0.7629 (tp) REVERT: A 432 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7989 (p) REVERT: F 42 LEU cc_start: 0.7025 (tt) cc_final: 0.6742 (tp) REVERT: F 97 TYR cc_start: 0.7792 (p90) cc_final: 0.7285 (p90) REVERT: F 147 MET cc_start: 0.5562 (ptp) cc_final: 0.5318 (pmm) REVERT: F 548 GLN cc_start: 0.6651 (tp-100) cc_final: 0.6190 (tm-30) REVERT: F 591 MET cc_start: 0.8762 (tmm) cc_final: 0.7970 (tmm) REVERT: F 592 MET cc_start: 0.7898 (mmm) cc_final: 0.7506 (mmm) outliers start: 66 outliers final: 60 residues processed: 237 average time/residue: 0.3794 time to fit residues: 151.4146 Evaluate side-chains 237 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 174 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 575 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 147 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain B residue 36 VAL 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 367 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 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 225 THR 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 382 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain A residue 36 VAL 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 363 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 36 VAL 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 280 VAL Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 0.2980 chunk 362 optimal weight: 0.9980 chunk 221 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 380 optimal weight: 8.9990 chunk 350 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** B 344 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29270 Z= 0.220 Angle : 0.538 11.482 39710 Z= 0.263 Chirality : 0.042 0.197 4762 Planarity : 0.003 0.042 5094 Dihedral : 6.315 71.817 4285 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 2.30 % Allowed : 19.00 % Favored : 78.71 % 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: -0.73 (0.14), residues: 3806 helix: 0.86 (0.14), residues: 1456 sheet: -1.95 (0.20), residues: 579 loop : -1.05 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 375 HIS 0.003 0.001 HIS C 93 PHE 0.016 0.001 PHE D 306 TYR 0.035 0.001 TYR F 531 ARG 0.008 0.000 ARG A 522 ********************** 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 245 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 179 time to evaluate : 3.314 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: 0.7871 (mpt-90) cc_final: 0.6772 (mmm160) REVERT: D 240 ILE cc_start: 0.6261 (pt) cc_final: 0.5949 (pt) REVERT: D 612 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8028 (pttp) REVERT: C 92 VAL cc_start: 0.6339 (OUTLIER) cc_final: 0.5957 (p) REVERT: C 200 MET cc_start: 0.6137 (tpp) cc_final: 0.5922 (mmt) REVERT: C 470 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 481 ILE cc_start: 0.8879 (tt) cc_final: 0.8505 (mt) REVERT: C 488 VAL cc_start: 0.8805 (t) cc_final: 0.8501 (p) REVERT: C 550 ILE cc_start: 0.8014 (mt) cc_final: 0.7802 (pt) REVERT: B 531 TYR cc_start: 0.8831 (t80) cc_final: 0.8540 (t80) REVERT: A 1 MET cc_start: 0.6985 (ptp) cc_final: 0.6339 (pmm) REVERT: A 195 LEU cc_start: 0.8023 (mt) cc_final: 0.7639 (tp) REVERT: F 42 LEU cc_start: 0.7038 (tt) cc_final: 0.6756 (tp) REVERT: F 97 TYR cc_start: 0.7798 (p90) cc_final: 0.7433 (p90) REVERT: F 147 MET cc_start: 0.5586 (ptp) cc_final: 0.5289 (pmm) REVERT: F 548 GLN cc_start: 0.6659 (tp-100) cc_final: 0.6357 (tm-30) outliers start: 66 outliers final: 61 residues processed: 235 average time/residue: 0.3732 time to fit residues: 146.8571 Evaluate side-chains 234 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 575 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 147 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 PHE 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 470 LEU Chi-restraints excluded: chain B residue 36 VAL 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 367 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 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 225 THR 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 382 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain A residue 36 VAL 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 363 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain F residue 36 VAL 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 280 VAL Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 0.9980 chunk 322 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 279 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 303 optimal weight: 0.0370 chunk 127 optimal weight: 50.0000 chunk 311 optimal weight: 40.0000 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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** B 344 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.133193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105396 restraints weight = 77065.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103408 restraints weight = 63481.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104287 restraints weight = 69191.352| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29270 Z= 0.155 Angle : 0.520 12.131 39710 Z= 0.255 Chirality : 0.041 0.217 4762 Planarity : 0.003 0.042 5094 Dihedral : 6.117 71.486 4285 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 2.19 % Allowed : 19.17 % Favored : 78.64 % 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: 0.96 (0.14), residues: 1455 sheet: -1.89 (0.20), residues: 593 loop : -0.97 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 375 HIS 0.002 0.000 HIS D 48 PHE 0.015 0.001 PHE B 186 TYR 0.019 0.001 TYR F 341 ARG 0.008 0.000 ARG A 522 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5459.79 seconds wall clock time: 101 minutes 9.15 seconds (6069.15 seconds total)