Starting phenix.real_space_refine on Thu Sep 18 07:49:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btu_44896/09_2025/9btu_44896_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btu_44896/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9btu_44896/09_2025/9btu_44896_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btu_44896/09_2025/9btu_44896_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9btu_44896/09_2025/9btu_44896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btu_44896/09_2025/9btu_44896.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'HIS:plan': 1, 'ASN:plan1': 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: 2.97, per 1000 atoms: 0.21 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: 1.30 Conformation dependent library (CDL) restraints added in 436.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.41 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: 3.19 Time building geometry restraints manager: 1.81 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: 7.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.020 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B 330 TYR 0.024 0.002 TYR B 335 PHE 0.033 0.003 PHE B 328 TRP 0.016 0.003 TRP C 229 HIS 0.010 0.003 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 8020) covalent geometry : angle 0.90272 (10906) SS BOND : bond 0.00362 ( 17) SS BOND : angle 1.16514 ( 34) hydrogen bonds : bond 0.18826 ( 306) hydrogen bonds : angle 9.42389 ( 816) link_BETA1-4 : bond 0.00530 ( 7) link_BETA1-4 : angle 4.53388 ( 21) link_NAG-ASN : bond 0.08230 ( 5) link_NAG-ASN : angle 5.30784 ( 15) *********************** 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 : 0.372 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: 0.2619 time to fit residues: 20.2896 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 : 0.334 ------------------------------------------------------------------------------- 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 49 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.080812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060637 restraints weight = 79820.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.063578 restraints weight = 34962.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065548 restraints weight = 21947.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066809 restraints weight = 16465.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.067657 restraints weight = 13732.308| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 8049 Z= 0.327 Angle : 0.788 7.979 10976 Z= 0.397 Chirality : 0.046 0.200 1276 Planarity : 0.004 0.041 1396 Dihedral : 10.208 56.586 1418 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.27), residues: 823 helix: -1.30 (0.32), residues: 215 sheet: -1.22 (0.35), residues: 189 loop : -0.96 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 490 TYR 0.017 0.002 TYR C 129 PHE 0.027 0.002 PHE B 328 TRP 0.014 0.002 TRP C 229 HIS 0.010 0.002 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 8020) covalent geometry : angle 0.77698 (10906) SS BOND : bond 0.00393 ( 17) SS BOND : angle 0.92417 ( 34) hydrogen bonds : bond 0.05306 ( 306) hydrogen bonds : angle 6.55071 ( 816) link_BETA1-4 : bond 0.00616 ( 7) link_BETA1-4 : angle 2.80383 ( 21) link_NAG-ASN : bond 0.00656 ( 5) link_NAG-ASN : angle 1.66378 ( 15) *********************** 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 41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9303 (t) cc_final: 0.8572 (p) REVERT: B 119 MET cc_start: 0.9133 (tpt) cc_final: 0.8929 (tpp) REVERT: B 238 MET cc_start: 0.8873 (mtt) cc_final: 0.8497 (mtm) REVERT: B 337 MET cc_start: 0.8125 (ttt) cc_final: 0.7576 (ttm) REVERT: C 351 MET cc_start: 0.8875 (mtt) cc_final: 0.8504 (mtt) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1648 time to fit residues: 9.4554 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 : 0.371 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.0570 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- 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 = 0.081988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061957 restraints weight = 79521.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064977 restraints weight = 33984.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067023 restraints weight = 20943.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068362 restraints weight = 15564.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069262 restraints weight = 12830.591| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8049 Z= 0.154 Angle : 0.608 6.345 10976 Z= 0.309 Chirality : 0.040 0.158 1276 Planarity : 0.004 0.043 1396 Dihedral : 7.672 47.301 1418 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.40 % Allowed : 4.97 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.29), residues: 823 helix: -0.06 (0.35), residues: 221 sheet: -1.15 (0.35), residues: 203 loop : -0.61 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 382 TYR 0.013 0.001 TYR B 358 PHE 0.021 0.001 PHE B 328 TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8020) covalent geometry : angle 0.59947 (10906) SS BOND : bond 0.00224 ( 17) SS BOND : angle 0.62848 ( 34) hydrogen bonds : bond 0.04200 ( 306) hydrogen bonds : angle 5.73505 ( 816) link_BETA1-4 : bond 0.00475 ( 7) link_BETA1-4 : angle 2.08581 ( 21) link_NAG-ASN : bond 0.00141 ( 5) link_NAG-ASN : angle 1.36371 ( 15) *********************** 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 42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9247 (t) cc_final: 0.8506 (p) REVERT: B 119 MET cc_start: 0.9127 (tpt) cc_final: 0.8894 (tpp) REVERT: B 238 MET cc_start: 0.8905 (mtt) cc_final: 0.8559 (mtm) REVERT: B 337 MET cc_start: 0.8070 (ttt) cc_final: 0.7717 (ttm) REVERT: C 351 MET cc_start: 0.8849 (mtt) cc_final: 0.8606 (mtt) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1585 time to fit residues: 9.5256 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 : 0.388 ------------------------------------------------------------------------------- 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 94 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.081664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061667 restraints weight = 79454.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.064662 restraints weight = 34597.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066696 restraints weight = 21563.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067988 restraints weight = 16093.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068856 restraints weight = 13359.924| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2506 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= 0.189 Angle : 0.579 5.633 10976 Z= 0.296 Chirality : 0.039 0.155 1276 Planarity : 0.004 0.046 1396 Dihedral : 6.602 46.503 1418 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.30), residues: 823 helix: 0.48 (0.36), residues: 221 sheet: -1.13 (0.35), residues: 204 loop : -0.56 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 125 TYR 0.013 0.001 TYR C 129 PHE 0.021 0.001 PHE B 328 TRP 0.012 0.002 TRP C 229 HIS 0.007 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8020) covalent geometry : angle 0.57329 (10906) SS BOND : bond 0.00254 ( 17) SS BOND : angle 0.79451 ( 34) hydrogen bonds : bond 0.03651 ( 306) hydrogen bonds : angle 5.36917 ( 816) link_BETA1-4 : bond 0.00365 ( 7) link_BETA1-4 : angle 1.55644 ( 21) link_NAG-ASN : bond 0.00250 ( 5) link_NAG-ASN : angle 1.33970 ( 15) *********************** 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 : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9205 (t) cc_final: 0.8443 (p) REVERT: B 119 MET cc_start: 0.9144 (tpt) cc_final: 0.8926 (tpp) REVERT: B 238 MET cc_start: 0.8906 (mtt) cc_final: 0.8483 (mtm) REVERT: B 240 TYR cc_start: 0.8482 (m-80) cc_final: 0.8034 (m-10) REVERT: B 337 MET cc_start: 0.8054 (ttt) cc_final: 0.7729 (ttm) REVERT: C 299 MET cc_start: 0.8457 (mmm) cc_final: 0.8193 (mmm) REVERT: C 351 MET cc_start: 0.8874 (mtt) cc_final: 0.8647 (mtt) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.1912 time to fit residues: 11.2427 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 : 0.378 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.081724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061629 restraints weight = 79951.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.064652 restraints weight = 34449.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066683 restraints weight = 21375.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.067998 restraints weight = 15940.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068858 restraints weight = 13223.627| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8049 Z= 0.177 Angle : 0.566 6.593 10976 Z= 0.289 Chirality : 0.038 0.152 1276 Planarity : 0.004 0.046 1396 Dihedral : 6.407 49.793 1418 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.27 % Allowed : 6.05 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.30), residues: 823 helix: 0.56 (0.36), residues: 221 sheet: -1.13 (0.34), residues: 212 loop : -0.47 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 388 TYR 0.012 0.001 TYR C 129 PHE 0.019 0.001 PHE B 328 TRP 0.011 0.001 TRP C 229 HIS 0.006 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8020) covalent geometry : angle 0.55896 (10906) SS BOND : bond 0.00301 ( 17) SS BOND : angle 1.02878 ( 34) hydrogen bonds : bond 0.03481 ( 306) hydrogen bonds : angle 5.25630 ( 816) link_BETA1-4 : bond 0.00375 ( 7) link_BETA1-4 : angle 1.45172 ( 21) link_NAG-ASN : bond 0.00220 ( 5) link_NAG-ASN : angle 1.25808 ( 15) *********************** 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 39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9214 (t) cc_final: 0.8408 (p) REVERT: B 119 MET cc_start: 0.9145 (tpt) cc_final: 0.8933 (tpp) REVERT: B 238 MET cc_start: 0.8897 (mtt) cc_final: 0.8493 (mtm) REVERT: B 240 TYR cc_start: 0.8464 (m-80) cc_final: 0.8099 (m-80) REVERT: B 337 MET cc_start: 0.8060 (ttt) cc_final: 0.7755 (ttm) REVERT: C 299 MET cc_start: 0.8419 (mmm) cc_final: 0.8153 (mmm) REVERT: C 351 MET cc_start: 0.8880 (mtt) cc_final: 0.8672 (mtt) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.1738 time to fit residues: 9.6266 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 : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN C 512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.081556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061397 restraints weight = 80601.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064414 restraints weight = 35063.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066435 restraints weight = 21871.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067712 restraints weight = 16401.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068564 restraints weight = 13652.969| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8049 Z= 0.186 Angle : 0.552 5.546 10976 Z= 0.282 Chirality : 0.038 0.149 1276 Planarity : 0.003 0.047 1396 Dihedral : 6.296 54.538 1418 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.67 % Allowed : 6.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.30), residues: 823 helix: 0.69 (0.36), residues: 221 sheet: -1.17 (0.34), residues: 213 loop : -0.40 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 479 TYR 0.012 0.001 TYR C 129 PHE 0.018 0.001 PHE B 328 TRP 0.011 0.001 TRP C 229 HIS 0.006 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8020) covalent geometry : angle 0.54583 (10906) SS BOND : bond 0.00290 ( 17) SS BOND : angle 0.86370 ( 34) hydrogen bonds : bond 0.03349 ( 306) hydrogen bonds : angle 5.19572 ( 816) link_BETA1-4 : bond 0.00389 ( 7) link_BETA1-4 : angle 1.44376 ( 21) link_NAG-ASN : bond 0.00229 ( 5) link_NAG-ASN : angle 1.20478 ( 15) *********************** 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 : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9206 (t) cc_final: 0.8480 (p) REVERT: B 238 MET cc_start: 0.8878 (mtt) cc_final: 0.8566 (mtm) REVERT: B 240 TYR cc_start: 0.8478 (m-80) cc_final: 0.8080 (m-10) REVERT: B 337 MET cc_start: 0.8077 (ttt) cc_final: 0.7755 (ttm) REVERT: C 299 MET cc_start: 0.8421 (mmm) cc_final: 0.8179 (mmm) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.1660 time to fit residues: 10.2094 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 : 0.433 ------------------------------------------------------------------------------- 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 63 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.081711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061590 restraints weight = 80547.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064612 restraints weight = 35083.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066625 restraints weight = 21945.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067924 restraints weight = 16416.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068728 restraints weight = 13634.759| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8049 Z= 0.162 Angle : 0.532 6.325 10976 Z= 0.271 Chirality : 0.038 0.168 1276 Planarity : 0.003 0.047 1396 Dihedral : 6.218 56.859 1418 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.30), residues: 823 helix: 0.81 (0.36), residues: 221 sheet: -1.15 (0.34), residues: 213 loop : -0.35 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 388 TYR 0.011 0.001 TYR C 129 PHE 0.017 0.001 PHE B 328 TRP 0.011 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8020) covalent geometry : angle 0.52756 (10906) SS BOND : bond 0.00230 ( 17) SS BOND : angle 0.66954 ( 34) hydrogen bonds : bond 0.03254 ( 306) hydrogen bonds : angle 5.15127 ( 816) link_BETA1-4 : bond 0.00295 ( 7) link_BETA1-4 : angle 1.37606 ( 21) link_NAG-ASN : bond 0.00171 ( 5) link_NAG-ASN : angle 1.13464 ( 15) *********************** 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 41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.424 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: 0.8428 (p) REVERT: B 238 MET cc_start: 0.8874 (mtt) cc_final: 0.8558 (mtm) REVERT: B 240 TYR cc_start: 0.8435 (m-80) cc_final: 0.8024 (m-80) REVERT: C 299 MET cc_start: 0.8399 (mmm) cc_final: 0.8171 (mmm) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.1254 time to fit residues: 8.0741 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 : 0.403 ------------------------------------------------------------------------------- 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 10 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.0050 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.081791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061645 restraints weight = 81245.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064677 restraints weight = 35170.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.066705 restraints weight = 21938.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068024 restraints weight = 16404.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068876 restraints weight = 13595.638| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8049 Z= 0.146 Angle : 0.516 6.681 10976 Z= 0.263 Chirality : 0.038 0.152 1276 Planarity : 0.003 0.046 1396 Dihedral : 6.074 58.453 1418 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.40 % Allowed : 6.99 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.31), residues: 823 helix: 0.97 (0.36), residues: 221 sheet: -1.12 (0.34), residues: 213 loop : -0.25 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 388 TYR 0.011 0.001 TYR B 273 PHE 0.016 0.001 PHE B 328 TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8020) covalent geometry : angle 0.51175 (10906) SS BOND : bond 0.00214 ( 17) SS BOND : angle 0.63954 ( 34) hydrogen bonds : bond 0.03144 ( 306) hydrogen bonds : angle 5.06960 ( 816) link_BETA1-4 : bond 0.00303 ( 7) link_BETA1-4 : angle 1.35446 ( 21) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 1.11005 ( 15) *********************** 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: 3 poor density : 38 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9180 (t) cc_final: 0.8418 (p) REVERT: B 238 MET cc_start: 0.8878 (mtt) cc_final: 0.8566 (mtm) REVERT: B 240 TYR cc_start: 0.8389 (m-80) cc_final: 0.8044 (m-80) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.1287 time to fit residues: 8.1175 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 : 0.382 ------------------------------------------------------------------------------- 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 1 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 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 = 0.3663 r_free = 0.3663 target = 0.081435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061306 restraints weight = 81318.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064307 restraints weight = 35384.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066308 restraints weight = 22078.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067610 restraints weight = 16522.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068461 restraints weight = 13711.133| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8049 Z= 0.192 Angle : 0.547 6.990 10976 Z= 0.277 Chirality : 0.038 0.148 1276 Planarity : 0.003 0.050 1396 Dihedral : 6.170 59.254 1418 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.54 % Allowed : 6.99 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.31), residues: 823 helix: 0.96 (0.36), residues: 221 sheet: -1.14 (0.34), residues: 215 loop : -0.33 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 172 TYR 0.012 0.001 TYR C 129 PHE 0.019 0.001 PHE B 328 TRP 0.010 0.001 TRP C 229 HIS 0.006 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8020) covalent geometry : angle 0.54193 (10906) SS BOND : bond 0.00253 ( 17) SS BOND : angle 0.67137 ( 34) hydrogen bonds : bond 0.03203 ( 306) hydrogen bonds : angle 5.12581 ( 816) link_BETA1-4 : bond 0.00315 ( 7) link_BETA1-4 : angle 1.42388 ( 21) link_NAG-ASN : bond 0.00224 ( 5) link_NAG-ASN : angle 1.10934 ( 15) *********************** 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 39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9189 (t) cc_final: 0.8422 (p) REVERT: B 238 MET cc_start: 0.8880 (mtt) cc_final: 0.8571 (mtm) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.1334 time to fit residues: 7.9183 Evaluate side-chains 38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 49 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.080313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060304 restraints weight = 81699.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063235 restraints weight = 35890.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.065194 restraints weight = 22510.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066435 restraints weight = 16890.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.067270 restraints weight = 14086.553| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8049 Z= 0.306 Angle : 0.656 10.654 10976 Z= 0.329 Chirality : 0.040 0.150 1276 Planarity : 0.004 0.060 1396 Dihedral : 6.566 59.368 1418 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.54 % Allowed : 6.99 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.30), residues: 823 helix: 0.76 (0.36), residues: 221 sheet: -1.33 (0.33), residues: 217 loop : -0.59 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 111 TYR 0.016 0.002 TYR C 129 PHE 0.022 0.002 PHE B 328 TRP 0.010 0.002 TRP C 229 HIS 0.009 0.002 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 8020) covalent geometry : angle 0.65125 (10906) SS BOND : bond 0.00363 ( 17) SS BOND : angle 0.77008 ( 34) hydrogen bonds : bond 0.03509 ( 306) hydrogen bonds : angle 5.36277 ( 816) link_BETA1-4 : bond 0.00364 ( 7) link_BETA1-4 : angle 1.57564 ( 21) link_NAG-ASN : bond 0.00456 ( 5) link_NAG-ASN : angle 1.25329 ( 15) ********************** 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 38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 SER cc_start: 0.9242 (t) cc_final: 0.8530 (p) REVERT: B 238 MET cc_start: 0.8877 (mtt) cc_final: 0.8535 (mtm) REVERT: B 239 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8870 (p) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.1314 time to fit residues: 7.5152 Evaluate side-chains 38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 43 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.081845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061760 restraints weight = 80515.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064778 restraints weight = 34997.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066794 restraints weight = 21799.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068091 restraints weight = 16291.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068936 restraints weight = 13516.036| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8049 Z= 0.117 Angle : 0.525 9.153 10976 Z= 0.262 Chirality : 0.037 0.154 1276 Planarity : 0.003 0.047 1396 Dihedral : 6.131 57.926 1418 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.67 % Allowed : 6.85 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.31), residues: 823 helix: 1.20 (0.37), residues: 215 sheet: -1.28 (0.33), residues: 219 loop : -0.22 (0.35), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 388 TYR 0.012 0.001 TYR B 273 PHE 0.011 0.001 PHE B 328 TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8020) covalent geometry : angle 0.52089 (10906) SS BOND : bond 0.00185 ( 17) SS BOND : angle 0.63337 ( 34) hydrogen bonds : bond 0.03108 ( 306) hydrogen bonds : angle 5.03925 ( 816) link_BETA1-4 : bond 0.00270 ( 7) link_BETA1-4 : angle 1.32555 ( 21) link_NAG-ASN : bond 0.00130 ( 5) link_NAG-ASN : angle 1.05733 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.06 seconds wall clock time: 47 minutes 49.02 seconds (2869.02 seconds total)