Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 17:10:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/04_2023/6vtl_21381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/04_2023/6vtl_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_21381/04_2023/6vtl_21381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/04_2023/6vtl_21381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/04_2023/6vtl_21381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtl_21381/04_2023/6vtl_21381.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 chiralities: 2 Time building chain proxies: 5.69, per 1000 atoms: 0.56 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: 3.95 Conformation dependent library (CDL) restraints added in 1.4 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: 0.80 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: 3.11 Time building geometry restraints manager: 4.30 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: 5609 17.86 - 35.71: 517 35.71 - 53.57: 72 53.57 - 71.43: 3 71.43 - 89.28: 18 Dihedral angle restraints: 6219 sinusoidal: 2310 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 6216 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: 8.400 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: 0.010 Extract box with map and model: 14.780 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.630 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.620 ------------------------------------------------------------------------------- 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 : 13.919 89.283 3648 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 % 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 *********************** 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 : 1.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1986 time to fit residues: 46.0531 Evaluate side-chains 99 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5074 ------------------------------------------------------------------------------- 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: 0.6980 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: 3.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 10482 Z= 0.388 Angle : 0.693 7.802 14256 Z= 0.358 Chirality : 0.045 0.156 1617 Planarity : 0.005 0.052 1839 Dihedral : 5.414 17.373 1446 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.46 % 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: -3.87 (0.21), residues: 1332 helix: -3.49 (0.16), residues: 447 sheet: -2.88 (0.29), residues: 285 loop : -1.38 (0.26), residues: 600 *********************** 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 134 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.222 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 125 average time/residue: 0.1704 time to fit residues: 33.7489 Evaluate side-chains 109 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1004 time to fit residues: 3.6721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN C 217 ASN B 217 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10482 Z= 0.241 Angle : 0.583 6.962 14256 Z= 0.294 Chirality : 0.042 0.155 1617 Planarity : 0.004 0.046 1839 Dihedral : 4.955 15.466 1446 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.97 % 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: -3.21 (0.21), residues: 1332 helix: -2.59 (0.19), residues: 444 sheet: -2.77 (0.28), residues: 285 loop : -1.16 (0.26), residues: 603 *********************** 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 131 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.338 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 0.1697 time to fit residues: 32.4633 Evaluate side-chains 111 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1016 time to fit residues: 4.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7037 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10482 Z= 0.195 Angle : 0.553 6.054 14256 Z= 0.278 Chirality : 0.041 0.171 1617 Planarity : 0.004 0.043 1839 Dihedral : 4.665 15.259 1446 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.87 % 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: -2.68 (0.22), residues: 1332 helix: -1.94 (0.21), residues: 444 sheet: -2.84 (0.28), residues: 267 loop : -0.90 (0.26), residues: 621 *********************** 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 140 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.254 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.1679 time to fit residues: 35.8167 Evaluate side-chains 117 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1034 time to fit residues: 3.8972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 398 GLN B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10482 Z= 0.225 Angle : 0.582 8.551 14256 Z= 0.287 Chirality : 0.042 0.192 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.653 20.055 1446 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.38 % 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: -2.38 (0.23), residues: 1332 helix: -1.50 (0.22), residues: 453 sheet: -2.75 (0.27), residues: 285 loop : -0.75 (0.28), residues: 594 *********************** 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 120 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.254 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.1709 time to fit residues: 31.3984 Evaluate side-chains 113 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0968 time to fit residues: 3.8542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 0.0050 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 42 optimal weight: 0.4980 chunk 67 optimal weight: 0.0970 chunk 123 optimal weight: 1.9990 overall best weight: 0.3372 ------------------------------------------------------------------------------- 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: 0.6979 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 10482 Z= 0.123 Angle : 0.557 8.082 14256 Z= 0.269 Chirality : 0.041 0.172 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.308 18.343 1446 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 1.38 % 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: -1.87 (0.23), residues: 1332 helix: -1.07 (0.23), residues: 462 sheet: -2.53 (0.28), residues: 267 loop : -0.49 (0.27), residues: 603 *********************** 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 121 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.251 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 112 average time/residue: 0.1736 time to fit residues: 30.8753 Evaluate side-chains 104 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1135 time to fit residues: 2.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.7064 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 10482 Z= 0.323 Angle : 0.630 14.152 14256 Z= 0.307 Chirality : 0.045 0.441 1617 Planarity : 0.004 0.040 1839 Dihedral : 4.624 16.864 1446 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 2.36 % 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: -1.90 (0.23), residues: 1332 helix: -0.79 (0.23), residues: 459 sheet: -2.81 (0.28), residues: 273 loop : -0.62 (0.28), residues: 600 *********************** 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 125 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.286 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 117 average time/residue: 0.1724 time to fit residues: 32.2975 Evaluate side-chains 107 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0996 time to fit residues: 4.0274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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: 0.6998 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 10482 Z= 0.152 Angle : 0.586 15.739 14256 Z= 0.277 Chirality : 0.043 0.414 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.334 15.972 1446 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 0.98 % 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: -1.43 (0.24), residues: 1332 helix: -0.45 (0.24), residues: 456 sheet: -2.54 (0.28), residues: 267 loop : -0.33 (0.28), residues: 609 *********************** 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 110 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.259 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 105 average time/residue: 0.1781 time to fit residues: 29.7410 Evaluate side-chains 104 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1103 time to fit residues: 2.2107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.7074 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.085 10482 Z= 0.366 Angle : 0.665 15.827 14256 Z= 0.323 Chirality : 0.046 0.461 1617 Planarity : 0.004 0.040 1839 Dihedral : 4.710 16.546 1446 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.69 % 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: -1.65 (0.24), residues: 1332 helix: -0.55 (0.24), residues: 459 sheet: -2.55 (0.30), residues: 240 loop : -0.72 (0.27), residues: 633 *********************** 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 109 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.360 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 105 average time/residue: 0.1751 time to fit residues: 29.4696 Evaluate side-chains 102 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1172 time to fit residues: 2.1456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7005 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10482 Z= 0.155 Angle : 0.582 9.376 14256 Z= 0.278 Chirality : 0.041 0.179 1617 Planarity : 0.004 0.041 1839 Dihedral : 4.393 16.073 1446 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.88 % 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: -1.29 (0.24), residues: 1332 helix: -0.23 (0.25), residues: 444 sheet: -2.58 (0.28), residues: 267 loop : -0.28 (0.27), residues: 621 ********************** 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 109 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.304 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.1796 time to fit residues: 30.5526 Evaluate side-chains 103 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1050 time to fit residues: 2.6487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4668 r_free = 0.4668 target = 0.172378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.131149 restraints weight = 20546.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.133290 restraints weight = 12889.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.135783 restraints weight = 9417.141| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 10482 Z= 0.146 Angle : 0.578 9.824 14256 Z= 0.271 Chirality : 0.041 0.166 1617 Planarity : 0.004 0.042 1839 Dihedral : 4.158 15.532 1446 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 : 0.29 % 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: -1.28 (0.24), residues: 1332 helix: -0.39 (0.24), residues: 474 sheet: -2.33 (0.29), residues: 258 loop : -0.30 (0.28), residues: 600 =============================================================================== Job complete usr+sys time: 1953.03 seconds wall clock time: 36 minutes 32.66 seconds (2192.66 seconds total)