Starting phenix.real_space_refine on Fri Jun 13 15:13:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btu_44896/06_2025/9btu_44896_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btu_44896/06_2025/9btu_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_44896/06_2025/9btu_44896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btu_44896/06_2025/9btu_44896.map" model { file = "/net/cci-nas-00/data/ceres_data/9btu_44896/06_2025/9btu_44896_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btu_44896/06_2025/9btu_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.27, per 1000 atoms: 0.58 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: 3.91 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: 1.45 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: 5.27 Time building geometry restraints manager: 4.48 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: 5.320 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: 0.300 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.050 Find NCS groups from input model: 0.180 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.580 ------------------------------------------------------------------------------- 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 0.088 8049 Z= 0.302 Angle : 0.944 12.844 10976 Z= 0.476 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 Details of bonding type rmsd link_NAG-ASN : bond 0.08230 ( 5) link_NAG-ASN : angle 5.30784 ( 15) link_BETA1-4 : bond 0.00530 ( 7) link_BETA1-4 : angle 4.53388 ( 21) hydrogen bonds : bond 0.18826 ( 306) hydrogen bonds : angle 9.42389 ( 816) SS BOND : bond 0.00362 ( 17) SS BOND : angle 1.16514 ( 34) covalent geometry : bond 0.00569 ( 8020) covalent geometry : angle 0.90272 (10906) *********************** 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 : 1.189 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: 0.5329 time to fit residues: 42.0257 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 : 1.154 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.081179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061077 restraints weight = 79213.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064035 restraints weight = 34643.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066003 restraints weight = 21700.755| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 8049 Z= 0.281 Angle : 0.755 7.811 10976 Z= 0.381 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 5) link_NAG-ASN : angle 1.65841 ( 15) link_BETA1-4 : bond 0.00677 ( 7) link_BETA1-4 : angle 2.68699 ( 21) hydrogen bonds : bond 0.05541 ( 306) hydrogen bonds : angle 6.52159 ( 816) SS BOND : bond 0.00344 ( 17) SS BOND : angle 0.89337 ( 34) covalent geometry : bond 0.00596 ( 8020) covalent geometry : angle 0.74432 (10906) *********************** 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 : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9299 (t) cc_final: 0.8605 (p) REVERT: B 119 MET cc_start: 0.9129 (tpt) cc_final: 0.8920 (tpp) REVERT: B 238 MET cc_start: 0.8851 (mtt) cc_final: 0.8494 (mtm) REVERT: B 337 MET cc_start: 0.8108 (ttt) cc_final: 0.7543 (ttm) REVERT: C 351 MET cc_start: 0.8866 (mtt) cc_final: 0.8509 (mtt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.3450 time to fit residues: 20.2396 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 : 1.029 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.082202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062124 restraints weight = 78627.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065153 restraints weight = 33714.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067202 restraints weight = 20833.629| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8049 Z= 0.147 Angle : 0.593 5.782 10976 Z= 0.301 Chirality : 0.039 0.152 1276 Planarity : 0.004 0.043 1396 Dihedral : 7.193 46.630 1418 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.84 (0.29), residues: 823 helix: 0.14 (0.35), residues: 221 sheet: -1.07 (0.36), residues: 195 loop : -0.55 (0.32), residues: 407 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 0.019 0.001 PHE B 328 TYR 0.013 0.001 TYR B 358 ARG 0.003 0.000 ARG C 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 5) link_NAG-ASN : angle 1.35604 ( 15) link_BETA1-4 : bond 0.00447 ( 7) link_BETA1-4 : angle 1.85559 ( 21) hydrogen bonds : bond 0.04179 ( 306) hydrogen bonds : angle 5.59259 ( 816) SS BOND : bond 0.00236 ( 17) SS BOND : angle 0.63313 ( 34) covalent geometry : bond 0.00311 ( 8020) covalent geometry : angle 0.58622 (10906) *********************** 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 : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9253 (t) cc_final: 0.8604 (p) REVERT: B 119 MET cc_start: 0.9131 (tpt) cc_final: 0.8911 (tpp) REVERT: B 337 MET cc_start: 0.8073 (ttt) cc_final: 0.7735 (ttm) REVERT: C 351 MET cc_start: 0.8869 (mtt) cc_final: 0.8653 (mtt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.3573 time to fit residues: 21.0010 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 : 1.113 ------------------------------------------------------------------------------- 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 71 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.081702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061641 restraints weight = 79394.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064684 restraints weight = 34095.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066757 restraints weight = 21090.487| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8049 Z= 0.180 Angle : 0.570 5.779 10976 Z= 0.290 Chirality : 0.038 0.156 1276 Planarity : 0.003 0.045 1396 Dihedral : 6.385 47.472 1418 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.40 % Allowed : 5.51 % Favored : 94.09 % 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: -0.57 (0.30), residues: 823 helix: 0.67 (0.37), residues: 215 sheet: -1.08 (0.35), residues: 207 loop : -0.43 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 229 HIS 0.006 0.001 HIS C 276 PHE 0.022 0.001 PHE B 328 TYR 0.012 0.001 TYR C 129 ARG 0.002 0.000 ARG B 479 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 5) link_NAG-ASN : angle 1.32847 ( 15) link_BETA1-4 : bond 0.00370 ( 7) link_BETA1-4 : angle 1.56578 ( 21) hydrogen bonds : bond 0.03501 ( 306) hydrogen bonds : angle 5.30018 ( 816) SS BOND : bond 0.00225 ( 17) SS BOND : angle 0.67344 ( 34) covalent geometry : bond 0.00384 ( 8020) covalent geometry : angle 0.56421 (10906) *********************** 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 43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9245 (t) cc_final: 0.8574 (p) REVERT: B 119 MET cc_start: 0.9142 (tpt) cc_final: 0.8930 (tpp) REVERT: B 337 MET cc_start: 0.8036 (ttt) cc_final: 0.7727 (ttm) REVERT: C 299 MET cc_start: 0.8455 (mmm) cc_final: 0.8164 (mmm) REVERT: C 351 MET cc_start: 0.8876 (mtt) cc_final: 0.8665 (mtt) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.3929 time to fit residues: 23.2027 Evaluate side-chains 39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 66 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.082505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062487 restraints weight = 80133.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065543 restraints weight = 33799.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.067624 restraints weight = 20785.181| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8049 Z= 0.124 Angle : 0.519 5.720 10976 Z= 0.267 Chirality : 0.038 0.151 1276 Planarity : 0.004 0.075 1396 Dihedral : 6.052 49.471 1418 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.54 % Allowed : 5.91 % Favored : 93.55 % 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: -0.35 (0.30), residues: 823 helix: 0.91 (0.37), residues: 215 sheet: -1.00 (0.34), residues: 211 loop : -0.29 (0.33), residues: 397 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 0.017 0.001 PHE B 328 TYR 0.009 0.001 TYR C 129 ARG 0.010 0.000 ARG B 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 5) link_NAG-ASN : angle 1.20417 ( 15) link_BETA1-4 : bond 0.00294 ( 7) link_BETA1-4 : angle 1.33305 ( 21) hydrogen bonds : bond 0.03273 ( 306) hydrogen bonds : angle 5.09640 ( 816) SS BOND : bond 0.00496 ( 17) SS BOND : angle 1.15949 ( 34) covalent geometry : bond 0.00267 ( 8020) covalent geometry : angle 0.51143 (10906) *********************** 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 41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9215 (t) cc_final: 0.8448 (p) REVERT: B 119 MET cc_start: 0.9133 (tpt) cc_final: 0.8910 (tpp) REVERT: B 240 TYR cc_start: 0.8426 (m-80) cc_final: 0.8108 (m-10) REVERT: B 337 MET cc_start: 0.8024 (ttt) cc_final: 0.7813 (ttm) REVERT: C 299 MET cc_start: 0.8443 (mmm) cc_final: 0.8165 (mmm) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.3531 time to fit residues: 20.6599 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 : 1.050 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.082315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062305 restraints weight = 79983.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.065367 restraints weight = 33789.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.067433 restraints weight = 20799.042| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8049 Z= 0.129 Angle : 0.508 5.723 10976 Z= 0.260 Chirality : 0.037 0.150 1276 Planarity : 0.004 0.059 1396 Dihedral : 5.864 52.218 1418 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.54 % Allowed : 5.91 % Favored : 93.55 % 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: -0.28 (0.30), residues: 823 helix: 0.96 (0.36), residues: 215 sheet: -0.94 (0.34), residues: 212 loop : -0.24 (0.34), residues: 396 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 0.017 0.001 PHE B 328 TYR 0.010 0.001 TYR C 129 ARG 0.008 0.000 ARG B 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 5) link_NAG-ASN : angle 1.18896 ( 15) link_BETA1-4 : bond 0.00286 ( 7) link_BETA1-4 : angle 1.37536 ( 21) hydrogen bonds : bond 0.03172 ( 306) hydrogen bonds : angle 5.01663 ( 816) SS BOND : bond 0.00215 ( 17) SS BOND : angle 0.78250 ( 34) covalent geometry : bond 0.00276 ( 8020) covalent geometry : angle 0.50244 (10906) *********************** 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 44 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9197 (t) cc_final: 0.8399 (p) REVERT: B 119 MET cc_start: 0.9135 (tpt) cc_final: 0.8911 (tpp) REVERT: B 240 TYR cc_start: 0.8439 (m-80) cc_final: 0.8146 (m-10) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.3659 time to fit residues: 23.2561 Evaluate side-chains 38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 22 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.081347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061216 restraints weight = 81026.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064207 restraints weight = 35249.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.066225 restraints weight = 22039.114| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8049 Z= 0.223 Angle : 0.567 6.017 10976 Z= 0.289 Chirality : 0.039 0.169 1276 Planarity : 0.004 0.051 1396 Dihedral : 6.141 56.905 1418 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -0.39 (0.30), residues: 823 helix: 0.89 (0.36), residues: 221 sheet: -1.11 (0.34), residues: 215 loop : -0.27 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.007 0.001 HIS C 276 PHE 0.020 0.001 PHE B 328 TYR 0.013 0.001 TYR C 129 ARG 0.007 0.000 ARG B 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 5) link_NAG-ASN : angle 1.21328 ( 15) link_BETA1-4 : bond 0.00374 ( 7) link_BETA1-4 : angle 1.49268 ( 21) hydrogen bonds : bond 0.03319 ( 306) hydrogen bonds : angle 5.17483 ( 816) SS BOND : bond 0.00291 ( 17) SS BOND : angle 0.76391 ( 34) covalent geometry : bond 0.00471 ( 8020) covalent geometry : angle 0.56184 (10906) *********************** 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 40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9251 (t) cc_final: 0.8558 (p) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.3215 time to fit residues: 19.2773 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 : 1.047 ------------------------------------------------------------------------------- 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 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.081812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061705 restraints weight = 80715.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064730 restraints weight = 35047.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066768 restraints weight = 21862.307| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8049 Z= 0.164 Angle : 0.522 6.324 10976 Z= 0.266 Chirality : 0.038 0.153 1276 Planarity : 0.003 0.047 1396 Dihedral : 6.070 59.276 1418 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.54 % Allowed : 6.45 % Favored : 93.01 % 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: -0.28 (0.31), residues: 823 helix: 0.98 (0.36), residues: 221 sheet: -1.11 (0.34), residues: 213 loop : -0.17 (0.35), residues: 389 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 0.014 0.001 PHE B 328 TYR 0.011 0.001 TYR C 129 ARG 0.006 0.000 ARG B 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 5) link_NAG-ASN : angle 1.12913 ( 15) link_BETA1-4 : bond 0.00259 ( 7) link_BETA1-4 : angle 1.36923 ( 21) hydrogen bonds : bond 0.03156 ( 306) hydrogen bonds : angle 5.05746 ( 816) SS BOND : bond 0.00227 ( 17) SS BOND : angle 0.67834 ( 34) covalent geometry : bond 0.00349 ( 8020) covalent geometry : angle 0.51744 (10906) *********************** 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: 4 poor density : 37 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9228 (t) cc_final: 0.8547 (p) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.3187 time to fit residues: 19.4088 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 : 1.174 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.082218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062111 restraints weight = 80937.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065181 restraints weight = 34873.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067201 restraints weight = 21661.779| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8049 Z= 0.131 Angle : 0.499 6.958 10976 Z= 0.253 Chirality : 0.037 0.157 1276 Planarity : 0.003 0.043 1396 Dihedral : 5.861 59.444 1418 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.17 (0.31), residues: 823 helix: 1.14 (0.36), residues: 221 sheet: -1.12 (0.33), residues: 218 loop : -0.06 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 PHE 0.014 0.001 PHE B 328 TYR 0.011 0.001 TYR B 273 ARG 0.004 0.000 ARG B 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 5) link_NAG-ASN : angle 1.07809 ( 15) link_BETA1-4 : bond 0.00266 ( 7) link_BETA1-4 : angle 1.33869 ( 21) hydrogen bonds : bond 0.03025 ( 306) hydrogen bonds : angle 4.96940 ( 816) SS BOND : bond 0.00190 ( 17) SS BOND : angle 0.64275 ( 34) covalent geometry : bond 0.00281 ( 8020) covalent geometry : angle 0.49435 (10906) *********************** 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 43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9190 (t) cc_final: 0.8432 (p) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.3028 time to fit residues: 19.5070 Evaluate side-chains 41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.082457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062361 restraints weight = 80964.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065430 restraints weight = 34854.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067484 restraints weight = 21630.199| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8049 Z= 0.115 Angle : 0.491 7.008 10976 Z= 0.248 Chirality : 0.037 0.154 1276 Planarity : 0.003 0.042 1396 Dihedral : 5.745 59.519 1418 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.40 % Allowed : 6.72 % 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: -0.00 (0.31), residues: 823 helix: 1.38 (0.37), residues: 215 sheet: -1.02 (0.33), residues: 218 loop : -0.02 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 PHE 0.013 0.001 PHE B 328 TYR 0.008 0.001 TYR B 326 ARG 0.005 0.000 ARG B 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 5) link_NAG-ASN : angle 1.06188 ( 15) link_BETA1-4 : bond 0.00255 ( 7) link_BETA1-4 : angle 1.31164 ( 21) hydrogen bonds : bond 0.02969 ( 306) hydrogen bonds : angle 4.89524 ( 816) SS BOND : bond 0.00171 ( 17) SS BOND : angle 0.60899 ( 34) covalent geometry : bond 0.00249 ( 8020) covalent geometry : angle 0.48662 (10906) ********************** 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 40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9186 (t) cc_final: 0.8428 (p) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.3169 time to fit residues: 19.5181 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 : 1.212 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.081689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061671 restraints weight = 81275.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064693 restraints weight = 35162.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.066712 restraints weight = 21862.477| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8049 Z= 0.191 Angle : 0.537 7.163 10976 Z= 0.271 Chirality : 0.037 0.147 1276 Planarity : 0.003 0.045 1396 Dihedral : 5.886 58.659 1418 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.54 % Allowed : 6.72 % 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: -0.23 (0.31), residues: 823 helix: 1.19 (0.37), residues: 221 sheet: -1.13 (0.33), residues: 219 loop : -0.19 (0.35), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.005 0.000 ARG B 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 5) link_NAG-ASN : angle 1.10976 ( 15) link_BETA1-4 : bond 0.00319 ( 7) link_BETA1-4 : angle 1.39998 ( 21) hydrogen bonds : bond 0.03091 ( 306) hydrogen bonds : angle 4.97846 ( 816) SS BOND : bond 0.00239 ( 17) SS BOND : angle 0.66203 ( 34) covalent geometry : bond 0.00404 ( 8020) covalent geometry : angle 0.53214 (10906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.05 seconds wall clock time: 78 minutes 39.60 seconds (4719.60 seconds total)