Starting phenix.real_space_refine on Sun Dec 29 03:33:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7r_27231/12_2024/8d7r_27231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7r_27231/12_2024/8d7r_27231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7r_27231/12_2024/8d7r_27231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7r_27231/12_2024/8d7r_27231.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7r_27231/12_2024/8d7r_27231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7r_27231/12_2024/8d7r_27231.cif" } resolution = 3.9 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= 0.018 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 36 5.16 5 C 6158 2.51 5 N 1608 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1607 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 20, 'TRANS': 178} Chain: "B" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3197 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 378} Chain breaks: 1 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 25, 'TRANS': 366} 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.25, per 1000 atoms: 0.65 Number of scatterers: 9627 At special positions: 0 Unit cell: (102.34, 144.48, 151.36, 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 36 16.00 O 1825 8.00 N 1608 7.00 C 6158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " 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=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 157 " " NAG A 703 " - " ASN A 383 " " NAG A 704 " - " ASN A 379 " " NAG B 901 " - " ASN B 426 " " NAG C 401 " - " ASN C 142 " " NAG E 1 " - " ASN C 190 " " NAG F 1 " - " ASN B 407 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 243 " " NAG I 1 " - " ASN A 227 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 21 sheets defined 12.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'D' and resid 35 through 65 removed outlier: 3.987A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 removed outlier: 3.699A pdb=" N ASN D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 66 through 71' Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.969A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 210 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AA2, first strand: chain 'C' and resid 211 through 214 Processing sheet with id=AA3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 147 removed outlier: 3.875A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 156 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 152 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP B 157 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS B 201 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.565A pdb=" N ASN B 191 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 175 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 177 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 242 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.720A pdb=" N ILE B 267 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 301 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 269 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 297 " --> pdb=" O CYS B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.652A pdb=" N ILE B 261 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 330 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 323 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 315 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 280 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 317 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 342 removed outlier: 5.712A pdb=" N GLN B 338 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN B 354 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN B 340 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 352 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.844A pdb=" N VAL B 380 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 371 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 409 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR B 406 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 425 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 421 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.688A pdb=" N ARG B 510 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 469 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 508 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 471 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 137 removed outlier: 7.684A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 194 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 196 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.527A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 229 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 243 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 231 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.781A pdb=" N MET A 302 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 258 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG A 300 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 260 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 298 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 262 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 296 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.905A pdb=" N VAL A 347 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 349 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.748A pdb=" N GLN A 378 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 403 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AC2, first strand: chain 'A' and resid 459 through 460 removed outlier: 4.019A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 469 through 474 removed outlier: 3.568A pdb=" N ASP A 469 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 512 " --> pdb=" O TYR A 492 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 585 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: 2.58 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3010 1.34 - 1.46: 2438 1.46 - 1.58: 4403 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 9899 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+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 2.21e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 9894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13120 1.41 - 2.82: 318 2.82 - 4.23: 53 4.23 - 5.63: 10 5.63 - 7.04: 7 Bond angle restraints: 13508 Sorted by residual: angle pdb=" C PRO A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ALA B 448 " pdb=" N VAL B 449 " pdb=" CA VAL B 449 " ideal model delta sigma weight residual 120.49 125.19 -4.70 1.38e+00 5.25e-01 1.16e+01 angle pdb=" N ASN A 131 " pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " ideal model delta sigma weight residual 114.17 110.31 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA GLY A 361 " pdb=" C GLY A 361 " pdb=" N LYS A 362 " ideal model delta sigma weight residual 114.23 116.74 -2.51 8.80e-01 1.29e+00 8.14e+00 angle pdb=" C LEU B 194 " pdb=" N ASN B 195 " pdb=" CA ASN B 195 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.08e+00 ... (remaining 13503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 5767 21.88 - 43.76: 270 43.76 - 65.64: 57 65.64 - 87.52: 9 87.52 - 109.39: 26 Dihedral angle restraints: 6129 sinusoidal: 2682 harmonic: 3447 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 93.00 173.22 -80.22 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS A 458 " pdb=" SG CYS A 458 " pdb=" SG CYS A 466 " pdb=" CB CYS A 466 " ideal model delta sinusoidal sigma weight residual -86.00 -34.89 -51.11 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 60.67 32.33 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1270 0.049 - 0.098: 198 0.098 - 0.147: 76 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 190 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+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 -2.24 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1544 not shown) Planarity restraints: 1696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO D 67 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 501 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 272 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 273 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " 0.022 5.00e-02 4.00e+02 ... (remaining 1693 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3184 2.86 - 3.37: 8390 3.37 - 3.88: 14623 3.88 - 4.39: 15262 4.39 - 4.90: 26904 Nonbonded interactions: 68363 Sorted by model distance: nonbonded pdb=" NH1 ARG A 262 " pdb=" O THR A 263 " model vdw 2.345 3.120 nonbonded pdb=" O GLU D 92 " pdb=" OG SER D 96 " model vdw 2.348 3.040 nonbonded pdb=" O TYR A 257 " pdb=" OG1 THR A 277 " model vdw 2.370 3.040 nonbonded pdb=" OG SER B 374 " pdb=" O5 NAG F 1 " model vdw 2.375 3.040 nonbonded pdb=" OE1 GLU B 373 " pdb=" N SER B 376 " model vdw 2.380 3.120 ... (remaining 68358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.050 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.920 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 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 0.039 9899 Z= 0.173 Angle : 0.536 7.043 13508 Z= 0.271 Chirality : 0.042 0.245 1547 Planarity : 0.004 0.056 1685 Dihedral : 15.026 109.395 3865 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -3.25 (0.21), residues: 1157 helix: 1.59 (0.42), residues: 129 sheet: -1.70 (0.28), residues: 305 loop : -3.30 (0.17), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 146 HIS 0.001 0.000 HIS A 340 PHE 0.013 0.000 PHE A 332 TYR 0.011 0.001 TYR B 502 ARG 0.001 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.5426 (ptp) cc_final: 0.4966 (mpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2727 time to fit residues: 66.6576 Evaluate side-chains 99 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 0.0030 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS D 123 GLN D 135 HIS D 192 GLN C 162 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN C 256 HIS B 190 HIS B 201 HIS B 226 ASN B 286 ASN B 402 ASN B 420 GLN B 434 HIS B 454 HIS A 137 ASN A 287 GLN A 348 GLN A 471 GLN A 478 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9899 Z= 0.365 Angle : 0.864 13.680 13508 Z= 0.422 Chirality : 0.054 0.404 1547 Planarity : 0.006 0.073 1685 Dihedral : 11.808 86.757 1592 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.46 % Allowed : 14.46 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.95 (0.22), residues: 1157 helix: 1.59 (0.46), residues: 135 sheet: -1.90 (0.25), residues: 365 loop : -2.88 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 269 HIS 0.006 0.001 HIS B 344 PHE 0.041 0.003 PHE C 141 TYR 0.028 0.003 TYR D 49 ARG 0.005 0.001 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5760 (t0) REVERT: B 251 GLN cc_start: 0.6273 (tp-100) cc_final: 0.6008 (mm-40) REVERT: B 438 SER cc_start: 0.7949 (p) cc_final: 0.7720 (m) REVERT: A 213 ASN cc_start: 0.7828 (t0) cc_final: 0.7235 (p0) REVERT: A 351 TRP cc_start: 0.6663 (p90) cc_final: 0.5728 (p90) outliers start: 26 outliers final: 17 residues processed: 142 average time/residue: 0.2524 time to fit residues: 49.3524 Evaluate side-chains 117 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 HIS A 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9899 Z= 0.205 Angle : 0.666 10.345 13508 Z= 0.321 Chirality : 0.048 0.688 1547 Planarity : 0.004 0.042 1685 Dihedral : 9.676 79.828 1592 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.74 % Allowed : 16.64 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.47 (0.23), residues: 1157 helix: 2.49 (0.48), residues: 135 sheet: -1.63 (0.26), residues: 363 loop : -2.66 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 246 HIS 0.018 0.001 HIS A 478 PHE 0.012 0.001 PHE A 332 TYR 0.012 0.001 TYR A 322 ARG 0.007 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 245 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7328 (ptm160) REVERT: C 252 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5684 (t0) REVERT: A 328 LYS cc_start: 0.6604 (tmtt) cc_final: 0.6270 (tttm) REVERT: A 351 TRP cc_start: 0.6282 (p90) cc_final: 0.5674 (p90) REVERT: A 438 MET cc_start: 0.5464 (ptp) cc_final: 0.5206 (mpp) outliers start: 29 outliers final: 14 residues processed: 132 average time/residue: 0.2361 time to fit residues: 43.5534 Evaluate side-chains 115 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN D 180 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9899 Z= 0.237 Angle : 0.698 10.125 13508 Z= 0.335 Chirality : 0.047 0.460 1547 Planarity : 0.005 0.047 1685 Dihedral : 8.483 66.922 1592 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.78 % Allowed : 16.92 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.23 (0.24), residues: 1157 helix: 2.58 (0.48), residues: 135 sheet: -1.45 (0.27), residues: 362 loop : -2.48 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 519 HIS 0.015 0.001 HIS A 478 PHE 0.015 0.001 PHE A 332 TYR 0.012 0.001 TYR A 492 ARG 0.009 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.9000 (tt) cc_final: 0.8722 (tp) REVERT: C 245 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7405 (ptm160) REVERT: B 275 GLU cc_start: 0.7665 (mp0) cc_final: 0.7443 (mp0) REVERT: A 328 LYS cc_start: 0.6717 (tmtt) cc_final: 0.6411 (tttm) REVERT: A 351 TRP cc_start: 0.6652 (p90) cc_final: 0.6001 (p90) outliers start: 40 outliers final: 25 residues processed: 139 average time/residue: 0.2465 time to fit residues: 46.8810 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9899 Z= 0.182 Angle : 0.629 9.933 13508 Z= 0.304 Chirality : 0.045 0.474 1547 Planarity : 0.004 0.042 1685 Dihedral : 7.952 59.987 1592 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.74 % Allowed : 19.28 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.05 (0.24), residues: 1157 helix: 2.73 (0.47), residues: 135 sheet: -1.37 (0.27), residues: 361 loop : -2.34 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 246 HIS 0.003 0.000 HIS A 167 PHE 0.012 0.001 PHE A 332 TYR 0.020 0.001 TYR B 502 ARG 0.009 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8894 (tt) cc_final: 0.8638 (tp) REVERT: D 86 ARG cc_start: 0.6497 (mmt90) cc_final: 0.6283 (mmm160) REVERT: C 245 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7356 (ptm160) REVERT: A 206 LYS cc_start: 0.4102 (pptt) cc_final: 0.3228 (pptt) REVERT: A 328 LYS cc_start: 0.6548 (tmtt) cc_final: 0.6267 (tttm) REVERT: A 351 TRP cc_start: 0.6467 (p90) cc_final: 0.6032 (p90) REVERT: A 478 HIS cc_start: 0.5894 (OUTLIER) cc_final: 0.5573 (t-170) outliers start: 29 outliers final: 21 residues processed: 139 average time/residue: 0.2328 time to fit residues: 45.1754 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.6381 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9899 Z= 0.220 Angle : 0.649 11.728 13508 Z= 0.317 Chirality : 0.045 0.383 1547 Planarity : 0.005 0.046 1685 Dihedral : 7.552 53.734 1592 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 3.88 % Allowed : 18.90 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.97 (0.24), residues: 1157 helix: 2.82 (0.47), residues: 132 sheet: -1.32 (0.26), residues: 360 loop : -2.27 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 246 HIS 0.003 0.001 HIS A 167 PHE 0.013 0.001 PHE A 332 TYR 0.019 0.001 TYR A 322 ARG 0.012 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8951 (tt) cc_final: 0.8688 (tp) REVERT: C 245 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7450 (ptm160) REVERT: A 206 LYS cc_start: 0.4174 (pptt) cc_final: 0.3293 (pptt) REVERT: A 305 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7396 (p0) REVERT: A 328 LYS cc_start: 0.6797 (tmtt) cc_final: 0.6581 (tttm) REVERT: A 351 TRP cc_start: 0.6611 (p90) cc_final: 0.6130 (p90) REVERT: A 438 MET cc_start: 0.5478 (ptp) cc_final: 0.5189 (mpp) REVERT: A 478 HIS cc_start: 0.6010 (OUTLIER) cc_final: 0.5785 (t-170) outliers start: 41 outliers final: 25 residues processed: 135 average time/residue: 0.2440 time to fit residues: 45.8775 Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.0050 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9899 Z= 0.269 Angle : 0.721 13.666 13508 Z= 0.353 Chirality : 0.046 0.331 1547 Planarity : 0.005 0.043 1685 Dihedral : 7.271 54.636 1592 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.35 % Allowed : 18.71 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.09 (0.24), residues: 1157 helix: 2.93 (0.46), residues: 126 sheet: -1.42 (0.26), residues: 379 loop : -2.33 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 246 HIS 0.005 0.001 HIS B 291 PHE 0.018 0.002 PHE A 169 TYR 0.022 0.002 TYR B 502 ARG 0.010 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.9058 (tt) cc_final: 0.8734 (tp) REVERT: D 113 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8057 (mp) REVERT: D 133 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7079 (tp) REVERT: C 236 GLU cc_start: 0.6248 (mm-30) cc_final: 0.5981 (mm-30) REVERT: C 245 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7466 (ptm160) REVERT: A 206 LYS cc_start: 0.4759 (pptt) cc_final: 0.3705 (pptt) REVERT: A 328 LYS cc_start: 0.6825 (tmtt) cc_final: 0.6538 (tttm) REVERT: A 348 GLN cc_start: 0.7392 (tp-100) cc_final: 0.6953 (tt0) REVERT: A 351 TRP cc_start: 0.6932 (p90) cc_final: 0.6426 (p90) REVERT: A 438 MET cc_start: 0.5514 (ptp) cc_final: 0.5159 (mpp) outliers start: 46 outliers final: 32 residues processed: 147 average time/residue: 0.2401 time to fit residues: 48.8644 Evaluate side-chains 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.0050 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6513 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9899 Z= 0.243 Angle : 0.706 12.223 13508 Z= 0.350 Chirality : 0.046 0.297 1547 Planarity : 0.005 0.046 1685 Dihedral : 7.039 53.603 1592 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 3.50 % Allowed : 20.04 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.06 (0.24), residues: 1157 helix: 2.93 (0.45), residues: 126 sheet: -1.34 (0.26), residues: 367 loop : -2.34 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 232 HIS 0.003 0.001 HIS A 167 PHE 0.019 0.001 PHE A 332 TYR 0.011 0.001 TYR D 49 ARG 0.012 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.9034 (tt) cc_final: 0.8731 (tp) REVERT: D 113 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8051 (mp) REVERT: D 133 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7072 (tp) REVERT: D 154 LEU cc_start: 0.8610 (mm) cc_final: 0.8357 (mp) REVERT: C 236 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5906 (mm-30) REVERT: C 245 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7503 (ptm160) REVERT: A 206 LYS cc_start: 0.4749 (pptt) cc_final: 0.3718 (pptt) REVERT: A 328 LYS cc_start: 0.6795 (tmtt) cc_final: 0.6530 (tttm) REVERT: A 348 GLN cc_start: 0.7388 (tp-100) cc_final: 0.6989 (tt0) REVERT: A 351 TRP cc_start: 0.6804 (p90) cc_final: 0.6312 (p90) outliers start: 37 outliers final: 26 residues processed: 132 average time/residue: 0.2274 time to fit residues: 42.5142 Evaluate side-chains 129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6532 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9899 Z= 0.239 Angle : 0.696 11.704 13508 Z= 0.345 Chirality : 0.046 0.283 1547 Planarity : 0.005 0.053 1685 Dihedral : 6.863 53.802 1592 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 3.31 % Allowed : 20.42 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -2.02 (0.24), residues: 1157 helix: 2.98 (0.45), residues: 126 sheet: -1.29 (0.26), residues: 367 loop : -2.34 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 246 HIS 0.003 0.001 HIS A 226 PHE 0.018 0.001 PHE A 332 TYR 0.025 0.002 TYR A 322 ARG 0.013 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.9046 (tt) cc_final: 0.8737 (tp) REVERT: D 113 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8055 (mp) REVERT: D 133 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7081 (tp) REVERT: C 236 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5797 (mm-30) REVERT: C 245 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7420 (ptm160) REVERT: B 275 GLU cc_start: 0.7793 (mp0) cc_final: 0.7560 (mp0) REVERT: A 328 LYS cc_start: 0.6770 (tmtt) cc_final: 0.6552 (tttm) REVERT: A 348 GLN cc_start: 0.7299 (tp-100) cc_final: 0.7003 (tt0) REVERT: A 351 TRP cc_start: 0.6895 (p90) cc_final: 0.6386 (p90) REVERT: A 438 MET cc_start: 0.5478 (ptp) cc_final: 0.5266 (mpp) outliers start: 35 outliers final: 27 residues processed: 127 average time/residue: 0.2301 time to fit residues: 40.9843 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6391 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9899 Z= 0.176 Angle : 0.665 10.357 13508 Z= 0.329 Chirality : 0.045 0.270 1547 Planarity : 0.005 0.053 1685 Dihedral : 6.475 54.754 1592 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.36 % Allowed : 21.36 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.85 (0.24), residues: 1157 helix: 2.83 (0.46), residues: 132 sheet: -1.17 (0.27), residues: 363 loop : -2.21 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 254 HIS 0.004 0.001 HIS A 478 PHE 0.011 0.001 PHE A 332 TYR 0.010 0.001 TYR A 322 ARG 0.015 0.001 ARG A 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7944 (mp) REVERT: D 133 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7202 (tt) REVERT: D 154 LEU cc_start: 0.8606 (mm) cc_final: 0.8313 (mp) REVERT: C 236 GLU cc_start: 0.6117 (mm-30) cc_final: 0.5736 (mm-30) REVERT: B 275 GLU cc_start: 0.7679 (mp0) cc_final: 0.7456 (mp0) REVERT: A 328 LYS cc_start: 0.6908 (tmtt) cc_final: 0.6692 (tttm) REVERT: A 351 TRP cc_start: 0.6623 (p90) cc_final: 0.6299 (p90) outliers start: 25 outliers final: 18 residues processed: 123 average time/residue: 0.2297 time to fit residues: 40.1858 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.170086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.148941 restraints weight = 19035.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.148282 restraints weight = 25869.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149032 restraints weight = 22528.581| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9899 Z= 0.234 Angle : 0.697 10.024 13508 Z= 0.347 Chirality : 0.046 0.265 1547 Planarity : 0.005 0.058 1685 Dihedral : 6.561 54.886 1592 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.17 % Allowed : 22.02 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.96 (0.24), residues: 1157 helix: 2.62 (0.46), residues: 133 sheet: -1.24 (0.27), residues: 353 loop : -2.26 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 269 HIS 0.004 0.001 HIS C 147 PHE 0.013 0.001 PHE D 185 TYR 0.023 0.002 TYR A 322 ARG 0.013 0.001 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.58 seconds wall clock time: 41 minutes 30.85 seconds (2490.85 seconds total)