Starting phenix.real_space_refine on Tue Dec 31 07:36:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btu_44896/12_2024/9btu_44896_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btu_44896/12_2024/9btu_44896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9btu_44896/12_2024/9btu_44896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btu_44896/12_2024/9btu_44896.map" model { file = "/net/cci-nas-00/data/ceres_data/9btu_44896/12_2024/9btu_44896_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btu_44896/12_2024/9btu_44896_trim.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 61 5.16 5 C 4948 2.51 5 N 1321 2.21 5 O 1531 1.98 5 H 6422 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 14283 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 6644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6644 Classifications: {'peptide': 424} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 1 Chain: "D" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 6484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 6484 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 395} Chain breaks: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 365 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'TRANS': 72} Chain breaks: 3 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Time building chain proxies: 9.09, per 1000 atoms: 0.64 Number of scatterers: 14283 At special positions: 0 Unit cell: (109.858, 94.164, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 O 1531 8.00 N 1321 7.00 C 4948 6.00 H 6422 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 203 " distance=2.04 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 453 " distance=2.02 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 449 " distance=2.03 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 434 " distance=2.03 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 423 " 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 1 " - " ASN B 141 " " NAG B 701 " - " ASN B 449 " " NAG B 702 " - " ASN B 364 " " NAG B 703 " - " ASN B 378 " " NAG C 701 " - " ASN C 248 " Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 35.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 104 through 128 removed outlier: 5.772A pdb=" N HIS B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASP B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.928A pdb=" N TRP B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 228 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 372 through 378 removed outlier: 3.658A pdb=" N ASP B 376 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 Processing helix chain 'B' and resid 422 through 433 removed outlier: 3.710A pdb=" N LEU B 430 " --> pdb=" O CYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.676A pdb=" N ARG B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 480 Processing helix chain 'D' and resid 61 through 68 removed outlier: 5.742A pdb=" N UNK D 66 " --> pdb=" O UNK D 63 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N UNK D 68 " --> pdb=" O UNK D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'C' and resid 106 through 126 removed outlier: 4.905A pdb=" N HIS C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP C 116 " --> pdb=" O HIS C 112 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 221 through 239 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 430 through 444 Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.697A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.927A pdb=" N SER B 82 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 300 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE B 246 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.927A pdb=" N SER B 82 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 348 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N PHE B 502 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 11.720A pdb=" N LYS B 350 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N TYR B 504 " --> pdb=" O LYS B 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.518A pdb=" N MET B 90 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 266 Processing sheet with id=AA5, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.549A pdb=" N UNK D 18 " --> pdb=" O UNK D 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N UNK D 78 " --> pdb=" O UNK D 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N UNK D 69 " --> pdb=" O UNK D 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 86 removed outlier: 9.430A pdb=" N ARG C 514 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 359 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE C 516 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU C 361 " --> pdb=" O ILE C 516 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N GLU C 518 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE C 363 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 356 " --> pdb=" O THR C 465 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 265 through 266 removed outlier: 6.700A pdb=" N ILE C 309 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS C 260 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN C 307 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N MET C 351 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU C 505 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR C 353 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE C 507 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 355 " --> pdb=" O PHE C 507 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AB2, first strand: chain 'C' and resid 272 through 277 removed outlier: 6.752A pdb=" N ASN C 282 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASN C 101 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 172 through 173 removed outlier: 4.417A pdb=" N VAL C 202 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 6 309 hydrogen bonds defined for protein. 816 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: 4.71 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6422 1.03 - 1.23: 462 1.23 - 1.43: 2971 1.43 - 1.63: 4499 1.63 - 1.82: 88 Bond restraints: 14442 Sorted by residual: bond pdb=" N THR C 80 " pdb=" CA THR C 80 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.19e+00 bond pdb=" N GLU B 78 " pdb=" CA GLU B 78 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N UNK D 1 " pdb=" CA UNK D 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N UNK E 1 " pdb=" CA UNK E 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N THR C 80 " pdb=" H THR C 80 " ideal model delta sigma weight residual 0.860 0.892 -0.032 2.00e-02 2.50e+03 2.52e+00 ... (remaining 14437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 24664 1.71 - 3.41: 721 3.41 - 5.12: 93 5.12 - 6.82: 20 6.82 - 8.53: 4 Bond angle restraints: 25502 Sorted by residual: angle pdb=" N TRP C 431 " pdb=" CA TRP C 431 " pdb=" C TRP C 431 " ideal model delta sigma weight residual 110.97 117.50 -6.53 1.09e+00 8.42e-01 3.58e+01 angle pdb=" N ILE B 246 " pdb=" CA ILE B 246 " pdb=" C ILE B 246 " ideal model delta sigma weight residual 106.21 110.67 -4.46 1.07e+00 8.73e-01 1.74e+01 angle pdb=" C1 BMA I 3 " pdb=" O5 BMA I 3 " pdb=" C5 BMA I 3 " ideal model delta sigma weight residual 118.82 110.29 8.53 3.00e+00 1.11e-01 8.08e+00 angle pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " pdb=" C5 NAG J 1 " ideal model delta sigma weight residual 113.21 121.24 -8.03 3.00e+00 1.11e-01 7.16e+00 angle pdb=" C1 BMA A 3 " pdb=" O5 BMA A 3 " pdb=" C5 BMA A 3 " ideal model delta sigma weight residual 118.82 111.22 7.60 3.00e+00 1.11e-01 6.41e+00 ... (remaining 25497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 6820 21.13 - 42.27: 292 42.27 - 63.40: 119 63.40 - 84.54: 29 84.54 - 105.67: 16 Dihedral angle restraints: 7276 sinusoidal: 3712 harmonic: 3564 Sorted by residual: dihedral pdb=" CB CYS C 260 " pdb=" SG CYS C 260 " pdb=" SG CYS C 267 " pdb=" CB CYS C 267 " ideal model delta sinusoidal sigma weight residual -86.00 -168.07 82.07 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS C 394 " pdb=" SG CYS C 394 " pdb=" SG CYS C 453 " pdb=" CB CYS C 453 " ideal model delta sinusoidal sigma weight residual 93.00 170.05 -77.05 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS B 361 " pdb=" SG CYS B 361 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual 93.00 167.90 -74.90 1 1.00e+01 1.00e-02 7.10e+01 ... (remaining 7273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1039 0.058 - 0.116: 195 0.116 - 0.174: 34 0.174 - 0.231: 6 0.231 - 0.289: 2 Chirality restraints: 1276 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.53e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.57e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.28e+01 ... (remaining 1273 not shown) Planarity restraints: 2193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.045 2.00e-02 2.50e+03 3.76e-02 1.77e+01 pdb=" C7 NAG A 1 " -0.025 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.055 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 141 " 0.029 2.00e-02 2.50e+03 2.26e-02 7.69e+00 pdb=" CG ASN B 141 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 141 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 141 " -0.026 2.00e-02 2.50e+03 pdb="HD21 ASN B 141 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.030 2.00e-02 2.50e+03 2.46e-02 7.59e+00 pdb=" C7 NAG H 1 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.024 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.037 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.003 2.00e-02 2.50e+03 ... (remaining 2190 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 694 2.21 - 2.80: 26824 2.80 - 3.40: 35628 3.40 - 4.00: 46261 4.00 - 4.60: 71322 Nonbonded interactions: 180729 Sorted by model distance: nonbonded pdb=" OD1 ASN B 141 " pdb=" HG SER B 143 " model vdw 1.607 2.450 nonbonded pdb=" OE1 GLU C 341 " pdb=" H GLU C 341 " model vdw 1.648 2.450 nonbonded pdb=" OD2 ASP C 510 " pdb="HD21 ASN C 512 " model vdw 1.675 2.450 nonbonded pdb=" H ASP C 268 " pdb="HD21 ASN C 271 " model vdw 1.694 2.100 nonbonded pdb=" O VAL C 322 " pdb=" HG SER C 323 " model vdw 1.697 2.450 ... (remaining 180724 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 'A' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.110 Process input model: 34.670 Find NCS groups from input model: 0.150 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.006 0.039 8020 Z= 0.349 Angle : 0.903 8.527 10906 Z= 0.467 Chirality : 0.050 0.289 1276 Planarity : 0.005 0.061 1396 Dihedral : 15.431 105.672 3016 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.13 % Allowed : 1.21 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -2.60 (0.26), residues: 823 helix: -3.02 (0.25), residues: 221 sheet: -0.91 (0.35), residues: 186 loop : -1.26 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 229 HIS 0.010 0.003 HIS C 276 PHE 0.033 0.003 PHE B 328 TYR 0.024 0.002 TYR B 335 ARG 0.005 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9329 (t) cc_final: 0.8618 (p) REVERT: B 337 MET cc_start: 0.8046 (ttt) cc_final: 0.7522 (ttm) REVERT: C 351 MET cc_start: 0.8879 (mtt) cc_final: 0.8530 (mtt) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.5413 time to fit residues: 42.8166 Evaluate side-chains 38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8020 Z= 0.378 Angle : 0.744 7.811 10906 Z= 0.379 Chirality : 0.045 0.200 1276 Planarity : 0.004 0.042 1396 Dihedral : 10.140 56.654 1418 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.40 % Allowed : 4.44 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.63 (0.28), residues: 823 helix: -1.19 (0.32), residues: 215 sheet: -1.15 (0.35), residues: 189 loop : -0.86 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 229 HIS 0.009 0.002 HIS C 276 PHE 0.026 0.002 PHE B 328 TYR 0.016 0.002 TYR C 129 ARG 0.004 0.001 ARG C 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9292 (t) cc_final: 0.8599 (p) REVERT: B 119 MET cc_start: 0.9131 (tpt) cc_final: 0.8923 (tpp) REVERT: B 238 MET cc_start: 0.8852 (mtt) cc_final: 0.8499 (mtm) REVERT: B 337 MET cc_start: 0.8119 (ttt) cc_final: 0.7548 (ttm) REVERT: C 351 MET cc_start: 0.8863 (mtt) cc_final: 0.8501 (mtt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.3655 time to fit residues: 21.5209 Evaluate side-chains 38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8020 Z= 0.167 Angle : 0.584 6.272 10906 Z= 0.299 Chirality : 0.040 0.157 1276 Planarity : 0.004 0.040 1396 Dihedral : 7.510 46.807 1418 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.40 % Allowed : 4.70 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.30), residues: 823 helix: 0.20 (0.36), residues: 215 sheet: -1.11 (0.35), residues: 203 loop : -0.42 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS B 321 PHE 0.020 0.001 PHE B 328 TYR 0.013 0.001 TYR B 358 ARG 0.003 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9260 (t) cc_final: 0.8599 (p) REVERT: B 119 MET cc_start: 0.9134 (tpt) cc_final: 0.8918 (tpp) REVERT: B 337 MET cc_start: 0.8080 (ttt) cc_final: 0.7733 (ttm) REVERT: C 351 MET cc_start: 0.8846 (mtt) cc_final: 0.8622 (mtt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.3856 time to fit residues: 22.9761 Evaluate side-chains 38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8020 Z= 0.395 Angle : 0.673 5.369 10906 Z= 0.342 Chirality : 0.041 0.165 1276 Planarity : 0.004 0.050 1396 Dihedral : 7.113 47.813 1418 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.40 % Allowed : 5.65 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.09 (0.29), residues: 823 helix: 0.15 (0.36), residues: 221 sheet: -1.33 (0.36), residues: 202 loop : -0.77 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 229 HIS 0.010 0.002 HIS C 276 PHE 0.026 0.002 PHE B 328 TYR 0.017 0.002 TYR B 326 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9257 (t) cc_final: 0.8586 (p) REVERT: B 238 MET cc_start: 0.8878 (mtt) cc_final: 0.8550 (mtm) REVERT: B 337 MET cc_start: 0.8098 (ttt) cc_final: 0.7768 (ttm) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.4359 time to fit residues: 23.4044 Evaluate side-chains 37 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8020 Z= 0.177 Angle : 0.538 4.978 10906 Z= 0.277 Chirality : 0.038 0.153 1276 Planarity : 0.004 0.046 1396 Dihedral : 6.552 49.365 1418 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.40 % Allowed : 5.78 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.30), residues: 823 helix: 0.58 (0.36), residues: 221 sheet: -1.13 (0.34), residues: 211 loop : -0.43 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 PHE 0.016 0.001 PHE B 328 TYR 0.010 0.001 TYR C 217 ARG 0.006 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9235 (t) cc_final: 0.8520 (p) REVERT: B 238 MET cc_start: 0.8870 (mtt) cc_final: 0.8555 (mtm) REVERT: C 299 MET cc_start: 0.8427 (mmm) cc_final: 0.8174 (mmm) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.3753 time to fit residues: 22.0666 Evaluate side-chains 40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 432 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8020 Z= 0.268 Angle : 0.567 5.721 10906 Z= 0.292 Chirality : 0.039 0.148 1276 Planarity : 0.004 0.048 1396 Dihedral : 6.414 52.344 1418 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.67 % Allowed : 6.18 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.30), residues: 823 helix: 0.65 (0.36), residues: 221 sheet: -1.21 (0.34), residues: 213 loop : -0.44 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 229 HIS 0.006 0.001 HIS C 276 PHE 0.020 0.001 PHE B 328 TYR 0.012 0.001 TYR C 129 ARG 0.003 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9233 (t) cc_final: 0.8501 (p) REVERT: B 238 MET cc_start: 0.8872 (mtt) cc_final: 0.8563 (mtm) REVERT: C 299 MET cc_start: 0.8443 (mmm) cc_final: 0.8188 (mmm) REVERT: C 351 MET cc_start: 0.8931 (mtt) cc_final: 0.8698 (mtt) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.3731 time to fit residues: 22.7435 Evaluate side-chains 39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8020 Z= 0.211 Angle : 0.522 5.808 10906 Z= 0.269 Chirality : 0.038 0.151 1276 Planarity : 0.003 0.046 1396 Dihedral : 6.243 55.984 1418 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.54 % Allowed : 6.32 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.30), residues: 823 helix: 0.83 (0.36), residues: 221 sheet: -1.14 (0.34), residues: 212 loop : -0.33 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 PHE 0.016 0.001 PHE B 328 TYR 0.010 0.001 TYR C 217 ARG 0.004 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9219 (t) cc_final: 0.8517 (p) REVERT: B 238 MET cc_start: 0.8885 (mtt) cc_final: 0.8577 (mtm) REVERT: C 299 MET cc_start: 0.8412 (mmm) cc_final: 0.8174 (mmm) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.3753 time to fit residues: 22.6055 Evaluate side-chains 39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 512 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8020 Z= 0.256 Angle : 0.544 6.504 10906 Z= 0.278 Chirality : 0.038 0.173 1276 Planarity : 0.003 0.050 1396 Dihedral : 6.255 58.323 1418 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.67 % Allowed : 6.45 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 823 helix: 0.88 (0.36), residues: 221 sheet: -1.23 (0.33), residues: 215 loop : -0.33 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 229 HIS 0.006 0.001 HIS B 321 PHE 0.018 0.001 PHE B 328 TYR 0.012 0.001 TYR C 129 ARG 0.003 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9221 (t) cc_final: 0.8516 (p) REVERT: B 238 MET cc_start: 0.8873 (mtt) cc_final: 0.8563 (mtm) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.3141 time to fit residues: 19.1007 Evaluate side-chains 39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.0010 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8020 Z= 0.150 Angle : 0.493 6.828 10906 Z= 0.252 Chirality : 0.037 0.156 1276 Planarity : 0.003 0.043 1396 Dihedral : 6.009 59.996 1418 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.54 % Allowed : 6.59 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 823 helix: 1.19 (0.37), residues: 215 sheet: -1.15 (0.33), residues: 218 loop : -0.07 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 PHE 0.013 0.001 PHE B 328 TYR 0.009 0.001 TYR B 273 ARG 0.003 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9199 (t) cc_final: 0.8448 (p) REVERT: B 238 MET cc_start: 0.8868 (mtt) cc_final: 0.8563 (mtm) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.3062 time to fit residues: 20.0074 Evaluate side-chains 40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 49 optimal weight: 7.9990 chunk 63 optimal weight: 0.0040 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8020 Z= 0.186 Angle : 0.505 7.107 10906 Z= 0.257 Chirality : 0.037 0.155 1276 Planarity : 0.003 0.043 1396 Dihedral : 5.909 59.476 1418 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.67 % Allowed : 6.59 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.31), residues: 823 helix: 1.12 (0.36), residues: 221 sheet: -1.15 (0.33), residues: 219 loop : -0.12 (0.35), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 PHE 0.016 0.001 PHE B 328 TYR 0.010 0.001 TYR B 326 ARG 0.003 0.000 ARG B 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9189 (t) cc_final: 0.8432 (p) REVERT: B 238 MET cc_start: 0.8872 (mtt) cc_final: 0.8493 (mtm) outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.3069 time to fit residues: 18.7154 Evaluate side-chains 40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.082098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062239 restraints weight = 80368.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.065288 restraints weight = 34165.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.067306 restraints weight = 21089.493| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8020 Z= 0.157 Angle : 0.485 7.287 10906 Z= 0.246 Chirality : 0.037 0.151 1276 Planarity : 0.003 0.043 1396 Dihedral : 5.717 58.271 1418 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 6.59 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.31), residues: 823 helix: 1.36 (0.37), residues: 215 sheet: -1.04 (0.33), residues: 218 loop : -0.04 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 229 HIS 0.004 0.001 HIS B 321 PHE 0.014 0.001 PHE B 328 TYR 0.010 0.001 TYR B 273 ARG 0.003 0.000 ARG B 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2888.18 seconds wall clock time: 52 minutes 58.02 seconds (3178.02 seconds total)