Starting phenix.real_space_refine on Mon Mar 11 09:41:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6a_27221/03_2024/8d6a_27221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6a_27221/03_2024/8d6a_27221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6a_27221/03_2024/8d6a_27221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6a_27221/03_2024/8d6a_27221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6a_27221/03_2024/8d6a_27221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6a_27221/03_2024/8d6a_27221.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 32 5.16 5 C 5043 2.51 5 N 1321 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ASP 502": "OD1" <-> "OD2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7912 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain: "B" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3225 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 381} 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: "E" 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: "F" 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: "G" 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: "H" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.67, per 1000 atoms: 0.59 Number of scatterers: 7912 At special positions: 0 Unit cell: (104.06, 141.04, 160.82, 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 32 16.00 O 1516 8.00 N 1321 7.00 C 5043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 511 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 390 " " NAG A 703 " - " ASN A 157 " " NAG A 704 " - " ASN A 383 " " NAG A 705 " - " ASN A 379 " " NAG C 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 407 " " NAG F 1 " - " ASN B 426 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 243 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.4 seconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 21 sheets defined 13.8% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'D' and resid 43 through 70 Processing helix chain 'D' and resid 72 through 77 removed outlier: 4.404A pdb=" N ASN D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 77' Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 97 through 127 Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 176 through 202 removed outlier: 3.792A pdb=" N GLN D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.956A pdb=" N SER A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 144 removed outlier: 9.418A pdb=" N LYS A 221 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.733A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 196 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 removed outlier: 3.561A pdb=" N VAL A 207 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 226 through 232 removed outlier: 6.149A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 231 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 336 removed outlier: 3.790A pdb=" N ARG A 345 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 349 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 380 removed outlier: 3.573A pdb=" N LEU A 370 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 416 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.956A pdb=" N PHE A 433 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 440 " --> pdb=" O PHE A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 473 removed outlier: 3.556A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 497 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 473 removed outlier: 3.556A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 497 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 512 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 508 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AB4, first strand: chain 'B' and resid 143 through 147 removed outlier: 3.738A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 192 removed outlier: 3.837A pdb=" N ASN B 169 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 173 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 175 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 218 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 242 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.658A pdb=" N ILE B 267 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 301 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 297 " --> pdb=" O CYS B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 259 through 262 removed outlier: 6.299A pdb=" N LYS B 259 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY B 330 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE B 261 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 323 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 312 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 279 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.657A pdb=" N GLN B 337 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 354 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU B 339 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N SER B 352 " --> pdb=" O LEU B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 348 through 350 Processing sheet with id=AC1, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.627A pdb=" N TYR B 406 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 437 through 440 removed outlier: 3.761A pdb=" N HIS B 454 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE B 439 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 452 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.823A pdb=" N ARG B 480 " --> pdb=" O ILE B 468 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 648 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: 2.20 Time building geometry restraints manager: 3.35 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: 2485 1.35 - 1.47: 2021 1.47 - 1.59: 3565 1.59 - 1.71: 0 1.71 - 1.83: 40 Bond restraints: 8111 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 8106 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.48: 382 107.48 - 114.10: 4787 114.10 - 120.73: 2793 120.73 - 127.35: 2975 127.35 - 133.97: 112 Bond angle restraints: 11049 Sorted by residual: angle pdb=" C GLU A 151 " pdb=" N THR A 152 " pdb=" CA THR A 152 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LYS A 130 " pdb=" N ASN A 131 " pdb=" CA ASN A 131 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.96e+00 angle pdb=" C ASN A 131 " pdb=" N LEU A 132 " pdb=" CA LEU A 132 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.21e+00 angle pdb=" CA TYR D 67 " pdb=" CB TYR D 67 " pdb=" CG TYR D 67 " ideal model delta sigma weight residual 113.90 118.23 -4.33 1.80e+00 3.09e-01 5.78e+00 angle pdb=" N THR A 166 " pdb=" CA THR A 166 " pdb=" C THR A 166 " ideal model delta sigma weight residual 113.18 110.18 3.00 1.33e+00 5.65e-01 5.10e+00 ... (remaining 11044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 4729 21.50 - 43.00: 236 43.00 - 64.50: 55 64.50 - 86.00: 13 86.00 - 107.50: 34 Dihedral angle restraints: 5067 sinusoidal: 2227 harmonic: 2840 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 141.21 -48.21 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CA ASN A 131 " pdb=" C ASN A 131 " pdb=" N LEU A 132 " pdb=" CA LEU A 132 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA THR B 447 " pdb=" C THR B 447 " pdb=" N ALA B 448 " pdb=" CA ALA B 448 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1116 0.065 - 0.130: 168 0.130 - 0.195: 6 0.195 - 0.260: 0 0.260 - 0.324: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 390 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 131 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1289 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO B 501 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 325 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 326 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 445 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 446 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 446 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 446 " -0.019 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1725 2.79 - 3.32: 7108 3.32 - 3.84: 12077 3.84 - 4.37: 13247 4.37 - 4.90: 23412 Nonbonded interactions: 57569 Sorted by model distance: nonbonded pdb=" O ILE A 454 " pdb=" OG1 THR A 497 " model vdw 2.261 2.440 nonbonded pdb=" O HIS A 425 " pdb=" OH TYR A 500 " model vdw 2.263 2.440 nonbonded pdb=" O SER A 133 " pdb=" N GLU A 145 " model vdw 2.277 2.520 nonbonded pdb=" O ILE D 64 " pdb=" OG1 THR D 68 " model vdw 2.292 2.440 nonbonded pdb=" O SER B 473 " pdb=" OG SER B 473 " model vdw 2.302 2.440 ... (remaining 57564 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 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 13.460 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.150 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8111 Z= 0.180 Angle : 0.560 7.738 11049 Z= 0.288 Chirality : 0.044 0.324 1292 Planarity : 0.004 0.063 1374 Dihedral : 16.683 107.504 3196 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -3.01 (0.24), residues: 957 helix: 1.02 (0.44), residues: 124 sheet: -1.81 (0.27), residues: 308 loop : -2.98 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 517 HIS 0.004 0.000 HIS B 434 PHE 0.005 0.000 PHE A 332 TYR 0.017 0.001 TYR D 67 ARG 0.001 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8500 (p0) cc_final: 0.8173 (p0) REVERT: B 442 LYS cc_start: 0.7751 (tppt) cc_final: 0.7531 (tppt) REVERT: B 503 THR cc_start: 0.6822 (m) cc_final: 0.6186 (m) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2252 time to fit residues: 45.5136 Evaluate side-chains 90 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.0970 chunk 72 optimal weight: 0.0670 chunk 39 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN D 51 GLN D 54 GLN D 76 ASN D 150 ASN D 193 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 360 ASN A 404 ASN A 425 HIS B 190 HIS B 479 GLN B 527 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8111 Z= 0.170 Angle : 0.615 7.613 11049 Z= 0.301 Chirality : 0.046 0.300 1292 Planarity : 0.005 0.059 1374 Dihedral : 13.799 86.719 1346 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.18 % Allowed : 9.86 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -2.34 (0.25), residues: 957 helix: 2.10 (0.46), residues: 125 sheet: -1.51 (0.26), residues: 315 loop : -2.62 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 172 HIS 0.003 0.001 HIS B 434 PHE 0.012 0.001 PHE B 507 TYR 0.033 0.001 TYR A 396 ARG 0.005 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.5844 (mp) REVERT: A 177 ASP cc_start: 0.8504 (p0) cc_final: 0.8186 (p0) outliers start: 19 outliers final: 6 residues processed: 97 average time/residue: 0.1792 time to fit residues: 24.8926 Evaluate side-chains 83 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.0070 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 GLN A 153 HIS A 167 HIS A 258 ASN A 404 ASN A 478 HIS B 190 HIS B 251 GLN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8111 Z= 0.164 Angle : 0.592 9.002 11049 Z= 0.290 Chirality : 0.045 0.356 1292 Planarity : 0.004 0.057 1374 Dihedral : 10.254 77.602 1346 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.18 % Allowed : 13.53 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -2.00 (0.25), residues: 957 helix: 2.47 (0.46), residues: 125 sheet: -1.29 (0.25), residues: 329 loop : -2.43 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 172 HIS 0.004 0.001 HIS A 167 PHE 0.011 0.001 PHE A 297 TYR 0.022 0.001 TYR A 396 ARG 0.003 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8497 (p0) cc_final: 0.8171 (p0) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.1916 time to fit residues: 26.9737 Evaluate side-chains 94 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 503 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 86 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8111 Z= 0.165 Angle : 0.573 8.229 11049 Z= 0.286 Chirality : 0.045 0.343 1292 Planarity : 0.004 0.056 1374 Dihedral : 9.023 72.180 1346 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.52 % Allowed : 15.14 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -1.77 (0.26), residues: 957 helix: 2.42 (0.47), residues: 128 sheet: -1.09 (0.26), residues: 330 loop : -2.28 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 172 HIS 0.003 0.001 HIS B 190 PHE 0.011 0.001 PHE A 297 TYR 0.012 0.001 TYR B 406 ARG 0.004 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8496 (p0) cc_final: 0.8182 (p0) REVERT: A 452 LYS cc_start: 0.6996 (mmmt) cc_final: 0.6729 (mmtt) REVERT: B 442 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7346 (mmmt) outliers start: 22 outliers final: 15 residues processed: 102 average time/residue: 0.1980 time to fit residues: 27.9418 Evaluate side-chains 100 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 404 ASN A 478 HIS B 190 HIS B 251 GLN B 527 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8111 Z= 0.244 Angle : 0.637 13.682 11049 Z= 0.314 Chirality : 0.046 0.336 1292 Planarity : 0.005 0.059 1374 Dihedral : 8.462 66.436 1346 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.56 % Allowed : 15.94 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -1.73 (0.26), residues: 957 helix: 2.58 (0.46), residues: 121 sheet: -1.01 (0.26), residues: 335 loop : -2.27 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 333 HIS 0.006 0.001 HIS D 38 PHE 0.012 0.001 PHE A 297 TYR 0.013 0.002 TYR B 406 ARG 0.010 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8509 (p0) cc_final: 0.8137 (p0) REVERT: B 442 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7241 (mmmt) REVERT: B 453 TRP cc_start: 0.6199 (p90) cc_final: 0.5909 (p90) REVERT: B 469 GLU cc_start: 0.4742 (OUTLIER) cc_final: 0.4349 (pt0) outliers start: 31 outliers final: 21 residues processed: 104 average time/residue: 0.1998 time to fit residues: 28.8449 Evaluate side-chains 99 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8111 Z= 0.168 Angle : 0.589 8.635 11049 Z= 0.293 Chirality : 0.045 0.331 1292 Planarity : 0.004 0.054 1374 Dihedral : 8.100 63.636 1346 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.44 % Allowed : 16.06 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -1.58 (0.27), residues: 957 helix: 2.76 (0.48), residues: 121 sheet: -0.88 (0.27), residues: 328 loop : -2.20 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 172 HIS 0.004 0.001 HIS B 216 PHE 0.010 0.001 PHE A 297 TYR 0.022 0.001 TYR A 366 ARG 0.007 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8500 (p0) cc_final: 0.8099 (p0) REVERT: B 453 TRP cc_start: 0.6158 (p90) cc_final: 0.5914 (p90) REVERT: B 469 GLU cc_start: 0.4726 (OUTLIER) cc_final: 0.3913 (pt0) outliers start: 30 outliers final: 25 residues processed: 93 average time/residue: 0.1826 time to fit residues: 23.9496 Evaluate side-chains 99 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 73 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8111 Z= 0.223 Angle : 0.613 8.587 11049 Z= 0.308 Chirality : 0.045 0.332 1292 Planarity : 0.004 0.054 1374 Dihedral : 7.790 58.670 1346 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 3.56 % Allowed : 16.63 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.68 (0.27), residues: 957 helix: 2.00 (0.48), residues: 131 sheet: -0.90 (0.27), residues: 332 loop : -2.20 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 172 HIS 0.002 0.001 HIS B 216 PHE 0.010 0.001 PHE A 297 TYR 0.010 0.001 TYR B 406 ARG 0.010 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 469 GLU cc_start: 0.4832 (OUTLIER) cc_final: 0.4000 (pt0) outliers start: 31 outliers final: 22 residues processed: 88 average time/residue: 0.1966 time to fit residues: 24.3198 Evaluate side-chains 90 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 0.0040 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 404 ASN A 478 HIS B 190 HIS B 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8111 Z= 0.232 Angle : 0.620 8.957 11049 Z= 0.312 Chirality : 0.045 0.336 1292 Planarity : 0.004 0.052 1374 Dihedral : 7.558 56.037 1346 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.13 % Allowed : 16.86 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.67 (0.27), residues: 957 helix: 1.92 (0.47), residues: 131 sheet: -0.84 (0.27), residues: 334 loop : -2.21 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 172 HIS 0.011 0.001 HIS A 478 PHE 0.009 0.001 PHE A 297 TYR 0.010 0.001 TYR B 505 ARG 0.005 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 69 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7300 (mt) REVERT: A 452 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7128 (mmmm) REVERT: B 464 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6412 (t80) REVERT: B 469 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.4003 (pt0) outliers start: 36 outliers final: 27 residues processed: 93 average time/residue: 0.1803 time to fit residues: 23.6954 Evaluate side-chains 97 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 67 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.0570 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 0.0770 chunk 56 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8111 Z= 0.152 Angle : 0.607 9.560 11049 Z= 0.300 Chirality : 0.044 0.333 1292 Planarity : 0.004 0.055 1374 Dihedral : 7.182 53.235 1346 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.75 % Allowed : 18.69 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -1.47 (0.27), residues: 957 helix: 2.14 (0.48), residues: 131 sheet: -0.66 (0.28), residues: 329 loop : -2.14 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 470 HIS 0.003 0.000 HIS B 216 PHE 0.010 0.001 PHE A 297 TYR 0.030 0.001 TYR B 505 ARG 0.008 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 LYS cc_start: 0.7439 (mmmm) cc_final: 0.7067 (mmmm) outliers start: 24 outliers final: 23 residues processed: 89 average time/residue: 0.1772 time to fit residues: 22.8741 Evaluate side-chains 88 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 0.0010 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8111 Z= 0.183 Angle : 0.610 9.760 11049 Z= 0.303 Chirality : 0.045 0.335 1292 Planarity : 0.004 0.055 1374 Dihedral : 7.034 55.043 1346 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 2.64 % Allowed : 19.04 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % 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: -1.50 (0.27), residues: 957 helix: 2.08 (0.48), residues: 131 sheet: -0.68 (0.28), residues: 334 loop : -2.16 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 470 HIS 0.003 0.001 HIS B 216 PHE 0.010 0.001 PHE A 297 TYR 0.011 0.001 TYR A 334 ARG 0.006 0.001 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LYS cc_start: 0.7463 (mmmm) cc_final: 0.7113 (mmmm) outliers start: 23 outliers final: 21 residues processed: 85 average time/residue: 0.1775 time to fit residues: 21.7729 Evaluate side-chains 89 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.119201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.096965 restraints weight = 22886.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097005 restraints weight = 15435.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.097610 restraints weight = 12036.464| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8111 Z= 0.189 Angle : 0.611 9.164 11049 Z= 0.304 Chirality : 0.044 0.336 1292 Planarity : 0.004 0.053 1374 Dihedral : 6.779 55.557 1346 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 2.41 % Allowed : 19.04 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.27), residues: 957 helix: 2.01 (0.48), residues: 131 sheet: -0.70 (0.28), residues: 336 loop : -2.14 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 470 HIS 0.003 0.001 HIS A 153 PHE 0.010 0.001 PHE A 297 TYR 0.037 0.001 TYR B 505 ARG 0.006 0.001 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.61 seconds wall clock time: 34 minutes 59.34 seconds (2099.34 seconds total)