Starting phenix.real_space_refine on Wed Feb 14 21:14:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/02_2024/6vtl_21381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/02_2024/6vtl_21381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/02_2024/6vtl_21381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/02_2024/6vtl_21381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/02_2024/6vtl_21381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/02_2024/6vtl_21381.pdb" } resolution = 3.65 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= 0.001 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 6591 2.51 5 N 1674 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C ASP 346": "OD1" <-> "OD2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 408": "OD1" <-> "OD2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 408": "OD1" <-> "OD2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10242 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3386 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 134 Chain: "C" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3386 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3386 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 134 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.85, per 1000 atoms: 0.57 Number of scatterers: 10242 At special positions: 0 Unit cell: (94.608, 97.2, 129.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 1896 8.00 N 1674 7.00 C 6591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 195 " distance=2.04 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 366 " distance=2.04 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 362 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 366 " distance=2.04 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 336 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 394 " " NAG A 602 " - " ASN A 367 " " NAG B 601 " - " ASN B 394 " " NAG B 602 " - " ASN B 367 " " NAG C 601 " - " ASN C 394 " " NAG C 602 " - " ASN C 367 " Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 2.1 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 41.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.653A pdb=" N SER A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 41 through 53 removed outlier: 4.149A pdb=" N VAL A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.671A pdb=" N VAL A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.628A pdb=" N ALA A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 removed outlier: 3.731A pdb=" N ILE A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.778A pdb=" N TYR A 230 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.622A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.698A pdb=" N ARG A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.716A pdb=" N GLU A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 removed outlier: 3.933A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.718A pdb=" N CYS A 360 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 392 removed outlier: 3.744A pdb=" N LYS A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.866A pdb=" N GLY A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 434 through 442 removed outlier: 3.962A pdb=" N LEU A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 removed outlier: 3.548A pdb=" N VAL A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.653A pdb=" N SER C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 41 through 53 removed outlier: 4.149A pdb=" N VAL C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.671A pdb=" N VAL C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.627A pdb=" N ALA C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.731A pdb=" N ILE C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.776A pdb=" N TYR C 230 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.622A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.697A pdb=" N ARG C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR C 317 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.717A pdb=" N GLU C 343 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.933A pdb=" N ASP C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.720A pdb=" N CYS C 360 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 392 removed outlier: 3.745A pdb=" N LYS C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.866A pdb=" N GLY C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.962A pdb=" N LEU C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.549A pdb=" N VAL C 449 " --> pdb=" O SER C 445 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.652A pdb=" N SER B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 41 through 53 removed outlier: 4.149A pdb=" N VAL B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 removed outlier: 3.671A pdb=" N VAL B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.627A pdb=" N ALA B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 removed outlier: 3.732A pdb=" N ILE B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.777A pdb=" N TYR B 230 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.622A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.698A pdb=" N ARG B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.716A pdb=" N GLU B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.933A pdb=" N ASP B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 351 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.719A pdb=" N CYS B 360 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 392 removed outlier: 3.745A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.867A pdb=" N GLY B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.961A pdb=" N LEU B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 460 removed outlier: 3.548A pdb=" N VAL B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A 270 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 406 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 410 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 405 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 277 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.842A pdb=" N LYS A 194 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN A 95 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 251 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 246 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA6, first strand: chain 'C' and resid 74 through 82 removed outlier: 8.527A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE C 270 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 406 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 410 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 405 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 82 removed outlier: 8.527A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 277 " --> pdb=" O GLY C 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.843A pdb=" N LYS C 194 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN C 95 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS C 251 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 246 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE B 270 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 406 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 410 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 405 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 74 through 82 removed outlier: 8.526A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 277 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 190 removed outlier: 6.843A pdb=" N LYS B 194 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN B 95 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS B 251 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 246 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 175 426 hydrogen bonds defined for protein. 1179 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: 3.28 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3300 1.35 - 1.47: 2614 1.47 - 1.59: 4457 1.59 - 1.72: 0 1.72 - 1.84: 111 Bond restraints: 10482 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" CB GLU A 137 " pdb=" CG GLU A 137 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB GLU C 137 " pdb=" CG GLU C 137 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.22e+00 ... (remaining 10477 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.41: 305 106.41 - 113.29: 5470 113.29 - 120.17: 3860 120.17 - 127.05: 4534 127.05 - 133.93: 87 Bond angle restraints: 14256 Sorted by residual: angle pdb=" CA GLY C 245 " pdb=" C GLY C 245 " pdb=" N ILE C 246 " ideal model delta sigma weight residual 114.23 117.83 -3.60 8.80e-01 1.29e+00 1.67e+01 angle pdb=" CA GLY A 245 " pdb=" C GLY A 245 " pdb=" N ILE A 246 " ideal model delta sigma weight residual 114.23 117.80 -3.57 8.80e-01 1.29e+00 1.65e+01 angle pdb=" CA GLY B 245 " pdb=" C GLY B 245 " pdb=" N ILE B 246 " ideal model delta sigma weight residual 114.23 117.75 -3.52 8.80e-01 1.29e+00 1.60e+01 angle pdb=" CA CYS B 180 " pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " ideal model delta sigma weight residual 114.40 122.23 -7.83 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CA CYS C 180 " pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " ideal model delta sigma weight residual 114.40 122.17 -7.77 2.30e+00 1.89e-01 1.14e+01 ... (remaining 14251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5735 17.86 - 35.71: 517 35.71 - 53.57: 72 53.57 - 71.43: 3 71.43 - 89.28: 18 Dihedral angle restraints: 6345 sinusoidal: 2436 harmonic: 3909 Sorted by residual: dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 360 " pdb=" CB CYS B 360 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " pdb=" SG CYS C 360 " pdb=" CB CYS C 360 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual 93.00 178.28 -85.28 1 1.00e+01 1.00e-02 8.81e+01 ... (remaining 6342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 870 0.030 - 0.061: 431 0.061 - 0.091: 185 0.091 - 0.121: 92 0.121 - 0.152: 39 Chirality restraints: 1617 Sorted by residual: chirality pdb=" CA CYS B 366 " pdb=" N CYS B 366 " pdb=" C CYS B 366 " pdb=" CB CYS B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA CYS A 366 " pdb=" N CYS A 366 " pdb=" C CYS A 366 " pdb=" CB CYS A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CB ILE B 125 " pdb=" CA ILE B 125 " pdb=" CG1 ILE B 125 " pdb=" CG2 ILE B 125 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1614 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 125 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO B 126 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 125 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO C 126 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 125 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 126 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " 0.037 5.00e-02 4.00e+02 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3312 2.82 - 3.34: 8710 3.34 - 3.86: 16794 3.86 - 4.38: 19292 4.38 - 4.90: 32481 Nonbonded interactions: 80589 Sorted by model distance: nonbonded pdb=" OD1 ASN B 95 " pdb=" OH TYR B 230 " model vdw 2.306 2.440 nonbonded pdb=" OD1 ASN C 95 " pdb=" OH TYR C 230 " model vdw 2.306 2.440 nonbonded pdb=" OD1 ASN A 95 " pdb=" OH TYR A 230 " model vdw 2.307 2.440 nonbonded pdb=" NE1 TRP A 47 " pdb=" OD2 ASP C 454 " model vdw 2.332 2.520 nonbonded pdb=" O SER A 36 " pdb=" NH2 ARG A 44 " model vdw 2.349 2.520 ... (remaining 80584 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' selection = chain 'B' selection = chain 'C' } 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: 6.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.090 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 30.850 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 : 0.004 0.054 10482 Z= 0.265 Angle : 0.796 10.354 14256 Z= 0.423 Chirality : 0.048 0.152 1617 Planarity : 0.006 0.068 1839 Dihedral : 13.731 89.283 3774 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -4.96 (0.18), residues: 1332 helix: -4.73 (0.10), residues: 447 sheet: -3.46 (0.29), residues: 237 loop : -1.95 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 47 HIS 0.003 0.001 HIS A 29 PHE 0.013 0.001 PHE A 264 TYR 0.011 0.001 TYR B 416 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.222 Fit side-chains REVERT: A 57 LEU cc_start: 0.8200 (tp) cc_final: 0.7795 (tp) REVERT: A 139 LEU cc_start: 0.6892 (tt) cc_final: 0.6520 (mp) REVERT: A 277 GLN cc_start: 0.8650 (tp40) cc_final: 0.8074 (tp40) REVERT: A 329 MET cc_start: 0.8640 (mtt) cc_final: 0.8308 (mtp) REVERT: C 57 LEU cc_start: 0.8258 (tp) cc_final: 0.7811 (tp) REVERT: C 277 GLN cc_start: 0.8609 (tp40) cc_final: 0.8099 (tp40) REVERT: C 329 MET cc_start: 0.8585 (mtt) cc_final: 0.8110 (mtp) REVERT: B 57 LEU cc_start: 0.8149 (tp) cc_final: 0.7942 (tp) REVERT: B 101 PHE cc_start: 0.7788 (t80) cc_final: 0.7349 (t80) REVERT: B 139 LEU cc_start: 0.6813 (tt) cc_final: 0.6426 (mp) REVERT: B 277 GLN cc_start: 0.8632 (tp40) cc_final: 0.8093 (tp40) REVERT: B 329 MET cc_start: 0.8598 (mtt) cc_final: 0.8180 (mtp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1923 time to fit residues: 44.5458 Evaluate side-chains 103 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 10482 Z= 0.508 Angle : 0.755 9.072 14256 Z= 0.393 Chirality : 0.047 0.175 1617 Planarity : 0.005 0.051 1839 Dihedral : 5.604 18.980 1572 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.75 % Allowed : 15.04 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -4.02 (0.20), residues: 1332 helix: -3.44 (0.16), residues: 447 sheet: -3.22 (0.26), residues: 285 loop : -1.48 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 47 HIS 0.006 0.002 HIS A 164 PHE 0.015 0.002 PHE A 270 TYR 0.023 0.003 TYR B 393 ARG 0.003 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.224 Fit side-chains REVERT: A 57 LEU cc_start: 0.8184 (tp) cc_final: 0.7771 (tp) REVERT: A 139 LEU cc_start: 0.7311 (tt) cc_final: 0.6745 (mp) REVERT: A 277 GLN cc_start: 0.8550 (tp40) cc_final: 0.8123 (tp40) REVERT: A 329 MET cc_start: 0.8558 (mtt) cc_final: 0.8095 (mtp) REVERT: A 412 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 57 LEU cc_start: 0.8144 (tp) cc_final: 0.7711 (tp) REVERT: C 329 MET cc_start: 0.8509 (mtt) cc_final: 0.8036 (mtp) REVERT: B 57 LEU cc_start: 0.8176 (tp) cc_final: 0.7744 (tp) REVERT: B 101 PHE cc_start: 0.7955 (t80) cc_final: 0.7680 (t80) REVERT: B 277 GLN cc_start: 0.8560 (tp40) cc_final: 0.8008 (tp40) REVERT: B 329 MET cc_start: 0.8525 (mtt) cc_final: 0.8024 (mtp) outliers start: 28 outliers final: 16 residues processed: 129 average time/residue: 0.1658 time to fit residues: 33.8204 Evaluate side-chains 111 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 119 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 398 GLN C 217 ASN B 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10482 Z= 0.136 Angle : 0.555 6.679 14256 Z= 0.277 Chirality : 0.041 0.175 1617 Planarity : 0.004 0.047 1839 Dihedral : 4.752 16.434 1572 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.95 % Allowed : 13.96 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.06 (0.22), residues: 1332 helix: -2.53 (0.19), residues: 444 sheet: -2.64 (0.28), residues: 285 loop : -1.05 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.002 0.001 HIS C 111 PHE 0.012 0.001 PHE A 264 TYR 0.017 0.001 TYR C 416 ARG 0.001 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.050 Fit side-chains REVERT: A 57 LEU cc_start: 0.8061 (tp) cc_final: 0.7759 (tp) REVERT: A 92 THR cc_start: 0.8724 (m) cc_final: 0.8505 (t) REVERT: A 277 GLN cc_start: 0.8338 (tp40) cc_final: 0.7637 (tp40) REVERT: A 329 MET cc_start: 0.8551 (mtt) cc_final: 0.8230 (mtp) REVERT: C 57 LEU cc_start: 0.8102 (tp) cc_final: 0.7780 (tp) REVERT: C 329 MET cc_start: 0.8569 (mtt) cc_final: 0.8071 (mtp) REVERT: B 57 LEU cc_start: 0.8062 (tp) cc_final: 0.7734 (tp) REVERT: B 78 LEU cc_start: 0.8992 (mm) cc_final: 0.8792 (mm) REVERT: B 101 PHE cc_start: 0.7841 (t80) cc_final: 0.7620 (t80) REVERT: B 277 GLN cc_start: 0.8358 (tp40) cc_final: 0.7773 (tp40) REVERT: B 329 MET cc_start: 0.8578 (mtt) cc_final: 0.8234 (mtp) outliers start: 30 outliers final: 18 residues processed: 132 average time/residue: 0.1655 time to fit residues: 34.4826 Evaluate side-chains 128 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10482 Z= 0.382 Angle : 0.647 7.018 14256 Z= 0.327 Chirality : 0.044 0.159 1617 Planarity : 0.004 0.043 1839 Dihedral : 4.997 16.417 1572 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.13 % Allowed : 17.01 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.84 (0.22), residues: 1332 helix: -1.97 (0.21), residues: 447 sheet: -2.91 (0.27), residues: 285 loop : -1.01 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 47 HIS 0.003 0.001 HIS A 164 PHE 0.009 0.002 PHE C 441 TYR 0.017 0.002 TYR B 416 ARG 0.003 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.154 Fit side-chains REVERT: A 57 LEU cc_start: 0.8149 (tp) cc_final: 0.7807 (tp) REVERT: A 329 MET cc_start: 0.8562 (mtt) cc_final: 0.8123 (mtp) REVERT: A 417 GLU cc_start: 0.8490 (mp0) cc_final: 0.8163 (mp0) REVERT: C 57 LEU cc_start: 0.8155 (tp) cc_final: 0.7806 (tp) REVERT: C 96 LEU cc_start: 0.8824 (mt) cc_final: 0.8596 (mt) REVERT: C 329 MET cc_start: 0.8501 (mtt) cc_final: 0.8061 (mtp) REVERT: C 416 TYR cc_start: 0.8402 (p90) cc_final: 0.8177 (p90) REVERT: B 57 LEU cc_start: 0.8151 (tp) cc_final: 0.7771 (tp) REVERT: B 78 LEU cc_start: 0.9114 (mm) cc_final: 0.8901 (mm) REVERT: B 101 PHE cc_start: 0.7973 (t80) cc_final: 0.7755 (t80) REVERT: B 277 GLN cc_start: 0.8469 (tp40) cc_final: 0.7928 (tp40) REVERT: B 329 MET cc_start: 0.8487 (mtt) cc_final: 0.8046 (mtp) outliers start: 42 outliers final: 35 residues processed: 144 average time/residue: 0.1600 time to fit residues: 36.8153 Evaluate side-chains 139 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10482 Z= 0.210 Angle : 0.578 9.071 14256 Z= 0.286 Chirality : 0.042 0.175 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.816 22.904 1572 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.74 % Allowed : 18.39 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.40 (0.23), residues: 1332 helix: -1.51 (0.22), residues: 456 sheet: -2.81 (0.27), residues: 285 loop : -0.73 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.002 0.001 HIS C 111 PHE 0.012 0.001 PHE B 264 TYR 0.018 0.001 TYR B 416 ARG 0.001 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.250 Fit side-chains REVERT: A 57 LEU cc_start: 0.8067 (tp) cc_final: 0.7799 (tp) REVERT: A 329 MET cc_start: 0.8542 (mtt) cc_final: 0.8167 (mtp) REVERT: A 377 MET cc_start: 0.7618 (ttm) cc_final: 0.7392 (ttm) REVERT: A 417 GLU cc_start: 0.8452 (mp0) cc_final: 0.8141 (mp0) REVERT: C 57 LEU cc_start: 0.8051 (tp) cc_final: 0.7774 (tp) REVERT: C 329 MET cc_start: 0.8542 (mtt) cc_final: 0.8057 (mtp) REVERT: C 377 MET cc_start: 0.7538 (ttm) cc_final: 0.7310 (ttm) REVERT: C 416 TYR cc_start: 0.8461 (p90) cc_final: 0.8235 (p90) REVERT: B 57 LEU cc_start: 0.8073 (tp) cc_final: 0.7771 (tp) REVERT: B 78 LEU cc_start: 0.9109 (mm) cc_final: 0.8835 (mm) REVERT: B 101 PHE cc_start: 0.7891 (t80) cc_final: 0.7689 (t80) REVERT: B 277 GLN cc_start: 0.8382 (tp40) cc_final: 0.7840 (tp40) REVERT: B 329 MET cc_start: 0.8517 (mtt) cc_final: 0.8145 (mtp) REVERT: B 377 MET cc_start: 0.7544 (ttm) cc_final: 0.7316 (ttm) outliers start: 38 outliers final: 34 residues processed: 140 average time/residue: 0.1633 time to fit residues: 36.4309 Evaluate side-chains 141 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 107 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN C 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10482 Z= 0.198 Angle : 0.566 8.799 14256 Z= 0.277 Chirality : 0.042 0.190 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.621 17.872 1572 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.13 % Allowed : 18.49 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.12 (0.23), residues: 1332 helix: -1.11 (0.23), residues: 465 sheet: -2.73 (0.27), residues: 285 loop : -0.68 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.002 0.001 HIS A 164 PHE 0.010 0.001 PHE B 264 TYR 0.017 0.001 TYR B 416 ARG 0.002 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 107 time to evaluate : 1.230 Fit side-chains REVERT: A 57 LEU cc_start: 0.8068 (tp) cc_final: 0.7855 (tp) REVERT: A 329 MET cc_start: 0.8502 (mtt) cc_final: 0.8137 (mtp) REVERT: A 377 MET cc_start: 0.7599 (ttm) cc_final: 0.7331 (ttm) REVERT: A 417 GLU cc_start: 0.8554 (mp0) cc_final: 0.8196 (mp0) REVERT: C 57 LEU cc_start: 0.8067 (tp) cc_final: 0.7830 (tp) REVERT: C 329 MET cc_start: 0.8555 (mtt) cc_final: 0.8029 (mtp) REVERT: C 377 MET cc_start: 0.7484 (ttm) cc_final: 0.7205 (ttm) REVERT: B 57 LEU cc_start: 0.8103 (tp) cc_final: 0.7816 (tp) REVERT: B 78 LEU cc_start: 0.9137 (mm) cc_final: 0.8843 (mm) REVERT: B 329 MET cc_start: 0.8492 (mtt) cc_final: 0.8140 (mtp) REVERT: B 377 MET cc_start: 0.7527 (ttm) cc_final: 0.7251 (ttm) outliers start: 42 outliers final: 39 residues processed: 135 average time/residue: 0.1624 time to fit residues: 35.1452 Evaluate side-chains 141 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 102 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 0.0570 chunk 127 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10482 Z= 0.281 Angle : 0.598 7.464 14256 Z= 0.296 Chirality : 0.043 0.204 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.723 17.922 1572 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.62 % Allowed : 18.19 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.01 (0.23), residues: 1332 helix: -0.86 (0.23), residues: 465 sheet: -2.77 (0.28), residues: 285 loop : -0.71 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 47 HIS 0.002 0.001 HIS A 164 PHE 0.009 0.001 PHE B 264 TYR 0.018 0.002 TYR B 416 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 98 time to evaluate : 1.223 Fit side-chains REVERT: A 57 LEU cc_start: 0.8139 (tp) cc_final: 0.7890 (tp) REVERT: A 329 MET cc_start: 0.8551 (mtt) cc_final: 0.8184 (mtp) REVERT: A 377 MET cc_start: 0.7698 (ttm) cc_final: 0.7399 (ttm) REVERT: C 57 LEU cc_start: 0.8081 (tp) cc_final: 0.7835 (tp) REVERT: C 329 MET cc_start: 0.8501 (mtt) cc_final: 0.8094 (mtp) REVERT: C 377 MET cc_start: 0.7617 (ttm) cc_final: 0.7308 (ttm) REVERT: B 57 LEU cc_start: 0.8208 (tp) cc_final: 0.7999 (tp) REVERT: B 78 LEU cc_start: 0.9152 (mm) cc_final: 0.8830 (mm) REVERT: B 329 MET cc_start: 0.8528 (mtt) cc_final: 0.8155 (mtp) REVERT: B 377 MET cc_start: 0.7676 (ttm) cc_final: 0.7370 (ttm) outliers start: 47 outliers final: 38 residues processed: 133 average time/residue: 0.1591 time to fit residues: 33.9740 Evaluate side-chains 135 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 97 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 50.0000 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10482 Z= 0.184 Angle : 0.558 7.441 14256 Z= 0.273 Chirality : 0.042 0.188 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.531 17.127 1572 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.74 % Allowed : 19.17 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.76 (0.23), residues: 1332 helix: -0.64 (0.24), residues: 471 sheet: -2.64 (0.28), residues: 285 loop : -0.56 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.002 0.001 HIS C 328 PHE 0.010 0.001 PHE B 264 TYR 0.017 0.001 TYR B 416 ARG 0.001 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 100 time to evaluate : 1.263 Fit side-chains REVERT: A 57 LEU cc_start: 0.8097 (tp) cc_final: 0.7886 (tp) REVERT: A 329 MET cc_start: 0.8556 (mtt) cc_final: 0.8191 (mtp) REVERT: A 377 MET cc_start: 0.7588 (ttm) cc_final: 0.7289 (ttm) REVERT: A 417 GLU cc_start: 0.8490 (mp0) cc_final: 0.8203 (mp0) REVERT: C 57 LEU cc_start: 0.8045 (tp) cc_final: 0.7838 (tp) REVERT: C 329 MET cc_start: 0.8484 (mtt) cc_final: 0.8109 (mtp) REVERT: C 377 MET cc_start: 0.7503 (ttm) cc_final: 0.7212 (ttm) REVERT: B 57 LEU cc_start: 0.8160 (tp) cc_final: 0.7957 (tp) REVERT: B 78 LEU cc_start: 0.9140 (mm) cc_final: 0.8809 (mm) REVERT: B 234 TRP cc_start: 0.4755 (m-10) cc_final: 0.4480 (m-10) REVERT: B 329 MET cc_start: 0.8529 (mtt) cc_final: 0.8178 (mtp) REVERT: B 377 MET cc_start: 0.7530 (ttm) cc_final: 0.7235 (ttm) REVERT: B 416 TYR cc_start: 0.8458 (p90) cc_final: 0.8141 (p90) REVERT: B 417 GLU cc_start: 0.8157 (mp0) cc_final: 0.7952 (mp0) outliers start: 38 outliers final: 34 residues processed: 126 average time/residue: 0.1601 time to fit residues: 32.4908 Evaluate side-chains 131 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10482 Z= 0.267 Angle : 0.583 7.312 14256 Z= 0.289 Chirality : 0.042 0.176 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.608 16.568 1572 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.13 % Allowed : 19.08 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.72 (0.24), residues: 1332 helix: -0.53 (0.24), residues: 471 sheet: -2.68 (0.28), residues: 279 loop : -0.60 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 47 HIS 0.003 0.001 HIS C 328 PHE 0.019 0.001 PHE B 93 TYR 0.017 0.001 TYR B 416 ARG 0.002 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 1.175 Fit side-chains REVERT: A 57 LEU cc_start: 0.8137 (tp) cc_final: 0.7921 (tp) REVERT: A 329 MET cc_start: 0.8537 (mtt) cc_final: 0.8138 (mtp) REVERT: A 377 MET cc_start: 0.7672 (ttm) cc_final: 0.7356 (ttm) REVERT: C 57 LEU cc_start: 0.8088 (tp) cc_final: 0.7865 (tp) REVERT: C 329 MET cc_start: 0.8474 (mtt) cc_final: 0.7973 (mtp) REVERT: C 377 MET cc_start: 0.7624 (ttm) cc_final: 0.7306 (ttm) REVERT: B 78 LEU cc_start: 0.9147 (mm) cc_final: 0.8831 (mm) REVERT: B 234 TRP cc_start: 0.4760 (m-10) cc_final: 0.4500 (m-10) REVERT: B 329 MET cc_start: 0.8522 (mtt) cc_final: 0.8146 (mtp) REVERT: B 377 MET cc_start: 0.7641 (ttm) cc_final: 0.7316 (ttm) REVERT: B 416 TYR cc_start: 0.8499 (p90) cc_final: 0.8165 (p90) REVERT: B 417 GLU cc_start: 0.8349 (mp0) cc_final: 0.8087 (mp0) outliers start: 42 outliers final: 38 residues processed: 131 average time/residue: 0.1725 time to fit residues: 36.0929 Evaluate side-chains 135 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 97 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10482 Z= 0.170 Angle : 0.557 7.759 14256 Z= 0.271 Chirality : 0.042 0.195 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.415 16.132 1572 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.74 % Allowed : 19.96 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.52 (0.24), residues: 1332 helix: -0.39 (0.24), residues: 471 sheet: -2.56 (0.28), residues: 285 loop : -0.43 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 47 HIS 0.002 0.001 HIS B 29 PHE 0.018 0.001 PHE B 93 TYR 0.016 0.001 TYR B 416 ARG 0.001 0.000 ARG B 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 1.136 Fit side-chains REVERT: A 329 MET cc_start: 0.8496 (mtt) cc_final: 0.8145 (mtp) REVERT: A 377 MET cc_start: 0.7547 (ttm) cc_final: 0.7246 (ttm) REVERT: A 417 GLU cc_start: 0.8499 (mp0) cc_final: 0.8234 (mp0) REVERT: C 329 MET cc_start: 0.8523 (mtt) cc_final: 0.8169 (mtp) REVERT: C 377 MET cc_start: 0.7448 (ttm) cc_final: 0.7149 (ttm) REVERT: B 78 LEU cc_start: 0.9126 (mm) cc_final: 0.8818 (mm) REVERT: B 234 TRP cc_start: 0.4812 (m-10) cc_final: 0.4557 (m-10) REVERT: B 329 MET cc_start: 0.8576 (mtt) cc_final: 0.8270 (mtp) REVERT: B 377 MET cc_start: 0.7490 (ttm) cc_final: 0.7181 (ttm) REVERT: B 416 TYR cc_start: 0.8461 (p90) cc_final: 0.8210 (p90) REVERT: B 417 GLU cc_start: 0.8345 (mp0) cc_final: 0.8119 (mp0) outliers start: 38 outliers final: 36 residues processed: 132 average time/residue: 0.1540 time to fit residues: 32.6623 Evaluate side-chains 132 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.170681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.132802 restraints weight = 20662.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.133772 restraints weight = 13060.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.135017 restraints weight = 9146.514| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10482 Z= 0.186 Angle : 0.569 8.667 14256 Z= 0.273 Chirality : 0.042 0.201 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.359 15.183 1572 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.74 % Allowed : 20.65 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.40 (0.24), residues: 1332 helix: -0.27 (0.25), residues: 471 sheet: -2.50 (0.28), residues: 285 loop : -0.39 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 47 HIS 0.002 0.001 HIS C 328 PHE 0.017 0.001 PHE B 93 TYR 0.018 0.001 TYR C 283 ARG 0.001 0.000 ARG C 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.08 seconds wall clock time: 38 minutes 21.52 seconds (2301.52 seconds total)