Starting phenix.real_space_refine on Sun Apr 5 11:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p6s_71324/04_2026/9p6s_71324.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p6s_71324/04_2026/9p6s_71324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p6s_71324/04_2026/9p6s_71324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p6s_71324/04_2026/9p6s_71324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p6s_71324/04_2026/9p6s_71324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p6s_71324/04_2026/9p6s_71324.map" } resolution = 2.61 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= 0.000 sd= 0.001 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 Mn 7 7.51 5 S 39 5.16 5 C 6111 2.51 5 N 1615 2.21 5 O 2006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9778 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4567 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 39, 'TRANS': 561} Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3421 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1402 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 167} Chain: "D" 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' MN': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.35, per 1000 atoms: 0.24 Number of scatterers: 9778 At special positions: 0 Unit cell: (142.721, 123.182, 131.677, 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) Mn 7 24.99 S 39 16.00 O 2006 8.00 N 1615 7.00 C 6111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 6 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " BETA1-2 " MAN F 4 " - " NAG F 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 501 " - " ASN B 249 " " NAG B 502 " - " ASN B 386 " " NAG B 503 " - " ASN B 397 " " NAG B 504 " - " ASN B 192 " " NAG D 1 " - " ASN A 43 " " NAG E 1 " - " ASN A 266 " " NAG F 1 " - " ASN A 275 " " NAG G 1 " - " ASN A 141 " " NAG H 1 " - " ASN A 568 " " NAG I 1 " - " ASN A 256 " " NAG J 1 " - " ASN B 343 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 420.7 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 21 sheets defined 12.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 203 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.779A pdb=" N LYS A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.989A pdb=" N ASP B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 157 Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.950A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.031A pdb=" N GLY B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.534A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.481A pdb=" N ARG A 423 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 434 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLY A 421 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY A 436 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 419 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.711A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.778A pdb=" N THR A 104 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 134 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.640A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238 removed outlier: 3.705A pdb=" N PHE A 248 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.584A pdb=" N LEU A 340 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 359 removed outlier: 6.175A pdb=" N LEU A 355 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY A 372 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 370 " --> pdb=" O PRO A 357 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 359 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 400 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 389 through 390 Processing sheet with id=AB2, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.551A pdb=" N TYR A 549 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 528 through 536 Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.549A pdb=" N LYS B 70 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLN B 98 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 426 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 363 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 362 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER B 396 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 364 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS B 394 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 109 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 206 removed outlier: 6.786A pdb=" N VAL B 202 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N SER B 166 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER B 204 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 164 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 123 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLY B 163 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 125 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY B 165 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR B 127 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE B 167 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET B 129 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP B 124 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL B 255 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR B 126 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N SER B 257 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 128 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 258 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB8, first strand: chain 'C' and resid 1333 through 1336 Processing sheet with id=AB9, first strand: chain 'C' and resid 1371 through 1376 Processing sheet with id=AC1, first strand: chain 'C' and resid 1371 through 1376 Processing sheet with id=AC2, first strand: chain 'C' and resid 1421 through 1428 removed outlier: 7.065A pdb=" N LEU C1423 " --> pdb=" O ASP C1438 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASP C1438 " --> pdb=" O LEU C1423 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C1425 " --> pdb=" O SER C1436 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER C1436 " --> pdb=" O VAL C1425 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1461 through 1466 328 hydrogen bonds defined for protein. 855 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: 1.63 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3099 1.34 - 1.46: 2283 1.46 - 1.58: 4522 1.58 - 1.71: 0 1.71 - 1.83: 52 Bond restraints: 9956 Sorted by residual: bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" CB GLU C1364 " pdb=" CG GLU C1364 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" CB ASP A 31 " pdb=" CG ASP A 31 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CA ASP A 31 " pdb=" CB ASP A 31 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.54e-02 4.22e+03 1.52e+00 bond pdb=" CG ARG C1403 " pdb=" CD ARG C1403 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 ... (remaining 9951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 13276 2.37 - 4.74: 219 4.74 - 7.10: 20 7.10 - 9.47: 6 9.47 - 11.84: 3 Bond angle restraints: 13524 Sorted by residual: angle pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " pdb=" C5 NAG G 2 " ideal model delta sigma weight residual 113.21 125.05 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CB MET A 546 " pdb=" CG MET A 546 " pdb=" SD MET A 546 " ideal model delta sigma weight residual 112.70 124.46 -11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ILE B 94 " pdb=" CB ILE B 94 " pdb=" CG1 ILE B 94 " ideal model delta sigma weight residual 110.40 116.56 -6.16 1.70e+00 3.46e-01 1.31e+01 angle pdb=" CB LYS B 87 " pdb=" CG LYS B 87 " pdb=" CD LYS B 87 " ideal model delta sigma weight residual 111.30 119.38 -8.08 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CB MET A 464 " pdb=" CG MET A 464 " pdb=" SD MET A 464 " ideal model delta sigma weight residual 112.70 122.79 -10.09 3.00e+00 1.11e-01 1.13e+01 ... (remaining 13519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 5860 25.83 - 51.66: 334 51.66 - 77.48: 109 77.48 - 103.31: 20 103.31 - 129.14: 5 Dihedral angle restraints: 6328 sinusoidal: 2842 harmonic: 3486 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual -86.00 -171.37 85.37 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -153.81 67.81 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.10 44.90 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 6325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1400 0.083 - 0.166: 157 0.166 - 0.249: 11 0.249 - 0.332: 0 0.332 - 0.415: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" C2 MAN F 4 " pdb=" C1 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" O2 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.52 2.10 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 568 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1567 not shown) Planarity restraints: 1753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 275 " -0.036 2.00e-02 2.50e+03 3.28e-02 1.34e+01 pdb=" CG ASN A 275 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 275 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 275 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 397 " -0.027 2.00e-02 2.50e+03 2.64e-02 8.73e+00 pdb=" CG ASN B 397 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 397 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 397 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG B 503 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1403 " -0.233 9.50e-02 1.11e+02 1.05e-01 8.31e+00 pdb=" NE ARG C1403 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C1403 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C1403 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C1403 " -0.001 2.00e-02 2.50e+03 ... (remaining 1750 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 110 2.54 - 3.13: 7487 3.13 - 3.72: 15072 3.72 - 4.31: 22055 4.31 - 4.90: 35933 Nonbonded interactions: 80657 Sorted by model distance: nonbonded pdb="MN MN B 506 " pdb=" O HOH C1601 " model vdw 1.944 2.320 nonbonded pdb="MN MN B 505 " pdb=" O HOH B 609 " model vdw 1.978 2.320 nonbonded pdb="MN MN B 505 " pdb=" O HOH B 604 " model vdw 1.985 2.320 nonbonded pdb="MN MN B 506 " pdb=" O HOH B 601 " model vdw 1.986 2.320 nonbonded pdb="MN MN A 701 " pdb=" O HOH A 803 " model vdw 1.998 2.320 ... (remaining 80652 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = 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 individual isotropic 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: 9.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.050 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9996 Z= 0.150 Angle : 0.776 12.562 13631 Z= 0.357 Chirality : 0.050 0.415 1570 Planarity : 0.005 0.105 1742 Dihedral : 17.445 129.138 4073 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.68 % Allowed : 18.67 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.23), residues: 1218 helix: 1.42 (0.47), residues: 120 sheet: 0.54 (0.25), residues: 416 loop : -0.99 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C1403 TYR 0.016 0.002 TYR C1488 PHE 0.019 0.002 PHE B 423 TRP 0.023 0.002 TRP A 100 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9956) covalent geometry : angle 0.70430 (13524) SS BOND : bond 0.00171 ( 13) SS BOND : angle 0.80917 ( 26) hydrogen bonds : bond 0.13875 ( 314) hydrogen bonds : angle 7.67845 ( 855) link_ALPHA1-3 : bond 0.01324 ( 1) link_ALPHA1-3 : angle 0.32629 ( 3) link_ALPHA1-6 : bond 0.00997 ( 2) link_ALPHA1-6 : angle 2.36153 ( 6) link_BETA1-2 : bond 0.01080 ( 1) link_BETA1-2 : angle 5.60120 ( 3) link_BETA1-4 : bond 0.01286 ( 12) link_BETA1-4 : angle 3.81331 ( 36) link_NAG-ASN : bond 0.01100 ( 11) link_NAG-ASN : angle 4.99577 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.7685 (mt0) cc_final: 0.7409 (mm110) REVERT: B 38 MET cc_start: -0.0043 (mpt) cc_final: -0.0353 (mmp) REVERT: B 153 MET cc_start: 0.8294 (ttm) cc_final: 0.7854 (tmt) REVERT: B 418 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7764 (mmmm) REVERT: C 1380 ASN cc_start: 0.8448 (t0) cc_final: 0.8109 (t0) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.6497 time to fit residues: 35.5843 Evaluate side-chains 42 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 373 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.0060 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 overall best weight: 1.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 HIS ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 356 ASN C1362 HIS C1377 HIS C1386 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.083456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046522 restraints weight = 27538.140| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.37 r_work: 0.2663 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 9996 Z= 0.271 Angle : 0.779 11.472 13631 Z= 0.370 Chirality : 0.052 0.392 1570 Planarity : 0.005 0.053 1742 Dihedral : 12.740 110.633 1884 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.19 % Allowed : 14.31 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.38 (0.23), residues: 1218 helix: 1.59 (0.47), residues: 119 sheet: 0.46 (0.25), residues: 412 loop : -1.07 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1403 TYR 0.022 0.002 TYR C1488 PHE 0.016 0.002 PHE B 256 TRP 0.022 0.002 TRP A 100 HIS 0.010 0.002 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 9956) covalent geometry : angle 0.72273 (13524) SS BOND : bond 0.00234 ( 13) SS BOND : angle 0.82537 ( 26) hydrogen bonds : bond 0.05312 ( 314) hydrogen bonds : angle 6.35380 ( 855) link_ALPHA1-3 : bond 0.01600 ( 1) link_ALPHA1-3 : angle 1.42585 ( 3) link_ALPHA1-6 : bond 0.01471 ( 2) link_ALPHA1-6 : angle 2.52153 ( 6) link_BETA1-2 : bond 0.00871 ( 1) link_BETA1-2 : angle 7.00135 ( 3) link_BETA1-4 : bond 0.01173 ( 12) link_BETA1-4 : angle 3.55774 ( 36) link_NAG-ASN : bond 0.00889 ( 11) link_NAG-ASN : angle 4.07043 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 42 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.7956 (mt0) cc_final: 0.7655 (mm110) REVERT: A 409 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.9045 (t) REVERT: A 592 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7485 (t) REVERT: B 38 MET cc_start: 0.0060 (mpt) cc_final: -0.0273 (mmp) REVERT: B 92 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6628 (t70) REVERT: B 334 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7849 (mttp) REVERT: C 1373 ASP cc_start: 0.8894 (t0) cc_final: 0.8659 (t0) REVERT: C 1380 ASN cc_start: 0.8364 (t0) cc_final: 0.8030 (t0) outliers start: 33 outliers final: 13 residues processed: 69 average time/residue: 0.5234 time to fit residues: 39.3774 Evaluate side-chains 56 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.084346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047474 restraints weight = 27337.392| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.36 r_work: 0.2693 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9996 Z= 0.144 Angle : 0.671 11.623 13631 Z= 0.309 Chirality : 0.048 0.401 1570 Planarity : 0.004 0.053 1742 Dihedral : 12.000 103.760 1881 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.03 % Allowed : 15.57 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.27 (0.23), residues: 1218 helix: 1.64 (0.47), residues: 120 sheet: 0.57 (0.25), residues: 416 loop : -1.03 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.015 0.001 TYR C1488 PHE 0.018 0.002 PHE B 423 TRP 0.009 0.001 TRP A 188 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9956) covalent geometry : angle 0.61442 (13524) SS BOND : bond 0.00139 ( 13) SS BOND : angle 0.54614 ( 26) hydrogen bonds : bond 0.03950 ( 314) hydrogen bonds : angle 5.94472 ( 855) link_ALPHA1-3 : bond 0.01774 ( 1) link_ALPHA1-3 : angle 1.75038 ( 3) link_ALPHA1-6 : bond 0.01271 ( 2) link_ALPHA1-6 : angle 2.84053 ( 6) link_BETA1-2 : bond 0.00951 ( 1) link_BETA1-2 : angle 6.43098 ( 3) link_BETA1-4 : bond 0.01060 ( 12) link_BETA1-4 : angle 3.24383 ( 36) link_NAG-ASN : bond 0.00725 ( 11) link_NAG-ASN : angle 3.72377 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.7965 (mt0) cc_final: 0.7679 (mm110) REVERT: B 38 MET cc_start: 0.0124 (mpt) cc_final: -0.0199 (mmp) REVERT: B 86 LEU cc_start: 0.6633 (tp) cc_final: 0.5770 (pp) REVERT: C 1373 ASP cc_start: 0.8908 (t0) cc_final: 0.8673 (t0) REVERT: C 1380 ASN cc_start: 0.8352 (t0) cc_final: 0.8014 (t0) outliers start: 21 outliers final: 11 residues processed: 61 average time/residue: 0.5699 time to fit residues: 37.4715 Evaluate side-chains 51 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.083421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046502 restraints weight = 27534.443| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.36 r_work: 0.2665 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9996 Z= 0.197 Angle : 0.689 11.618 13631 Z= 0.321 Chirality : 0.049 0.398 1570 Planarity : 0.004 0.054 1742 Dihedral : 11.820 99.509 1881 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.71 % Allowed : 15.96 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.33 (0.23), residues: 1218 helix: 1.67 (0.47), residues: 119 sheet: 0.58 (0.26), residues: 407 loop : -1.10 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 551 TYR 0.016 0.002 TYR C1488 PHE 0.016 0.002 PHE B 423 TRP 0.009 0.001 TRP A 188 HIS 0.007 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9956) covalent geometry : angle 0.63487 (13524) SS BOND : bond 0.00158 ( 13) SS BOND : angle 0.60441 ( 26) hydrogen bonds : bond 0.04290 ( 314) hydrogen bonds : angle 5.78522 ( 855) link_ALPHA1-3 : bond 0.01636 ( 1) link_ALPHA1-3 : angle 1.90527 ( 3) link_ALPHA1-6 : bond 0.01283 ( 2) link_ALPHA1-6 : angle 2.85115 ( 6) link_BETA1-2 : bond 0.00961 ( 1) link_BETA1-2 : angle 6.65859 ( 3) link_BETA1-4 : bond 0.01027 ( 12) link_BETA1-4 : angle 3.11666 ( 36) link_NAG-ASN : bond 0.00746 ( 11) link_NAG-ASN : angle 3.76268 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8081 (mt0) cc_final: 0.7805 (mm110) REVERT: A 409 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (t) REVERT: B 38 MET cc_start: -0.0018 (mpt) cc_final: -0.0323 (mmp) REVERT: B 86 LEU cc_start: 0.6629 (tp) cc_final: 0.5597 (pt) REVERT: B 94 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.6045 (pp) REVERT: B 334 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8069 (mtpp) REVERT: C 1373 ASP cc_start: 0.8931 (t0) cc_final: 0.8689 (t0) REVERT: C 1380 ASN cc_start: 0.8342 (t0) cc_final: 0.8002 (t0) REVERT: C 1434 LEU cc_start: 0.8564 (tp) cc_final: 0.8358 (tm) outliers start: 28 outliers final: 15 residues processed: 64 average time/residue: 0.5969 time to fit residues: 41.1729 Evaluate side-chains 57 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 1365 HIS Chi-restraints excluded: chain C residue 1412 GLN Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 117 optimal weight: 0.0670 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.084092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046988 restraints weight = 27448.517| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.35 r_work: 0.2688 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9996 Z= 0.131 Angle : 0.647 11.296 13631 Z= 0.296 Chirality : 0.048 0.402 1570 Planarity : 0.004 0.054 1742 Dihedral : 11.282 97.122 1881 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.22 % Allowed : 16.73 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.24 (0.23), residues: 1218 helix: 1.65 (0.47), residues: 120 sheet: 0.67 (0.26), residues: 406 loop : -1.04 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.013 0.001 TYR C1488 PHE 0.013 0.001 PHE B 423 TRP 0.009 0.001 TRP A 188 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9956) covalent geometry : angle 0.59296 (13524) SS BOND : bond 0.00120 ( 13) SS BOND : angle 0.44878 ( 26) hydrogen bonds : bond 0.03529 ( 314) hydrogen bonds : angle 5.53280 ( 855) link_ALPHA1-3 : bond 0.01965 ( 1) link_ALPHA1-3 : angle 2.37080 ( 3) link_ALPHA1-6 : bond 0.01290 ( 2) link_ALPHA1-6 : angle 2.93101 ( 6) link_BETA1-2 : bond 0.00966 ( 1) link_BETA1-2 : angle 6.37555 ( 3) link_BETA1-4 : bond 0.01040 ( 12) link_BETA1-4 : angle 3.03952 ( 36) link_NAG-ASN : bond 0.00682 ( 11) link_NAG-ASN : angle 3.60708 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8068 (mt0) cc_final: 0.7776 (mm110) REVERT: B 38 MET cc_start: -0.0155 (mpt) cc_final: -0.0454 (mmp) REVERT: B 86 LEU cc_start: 0.6736 (tp) cc_final: 0.5651 (pt) REVERT: C 1373 ASP cc_start: 0.8920 (t0) cc_final: 0.8686 (t0) REVERT: C 1380 ASN cc_start: 0.8335 (t0) cc_final: 0.8006 (t0) outliers start: 23 outliers final: 11 residues processed: 62 average time/residue: 0.5453 time to fit residues: 36.8935 Evaluate side-chains 50 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 1365 HIS Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.083553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046653 restraints weight = 27352.210| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.32 r_work: 0.2675 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9996 Z= 0.150 Angle : 0.666 11.169 13631 Z= 0.305 Chirality : 0.048 0.399 1570 Planarity : 0.004 0.053 1742 Dihedral : 10.553 94.675 1881 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.22 % Allowed : 16.83 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.23 (0.23), residues: 1218 helix: 1.68 (0.47), residues: 120 sheet: 0.66 (0.25), residues: 410 loop : -1.04 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.014 0.001 TYR C1488 PHE 0.015 0.002 PHE A 569 TRP 0.009 0.001 TRP A 188 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9956) covalent geometry : angle 0.61398 (13524) SS BOND : bond 0.00131 ( 13) SS BOND : angle 0.47936 ( 26) hydrogen bonds : bond 0.03731 ( 314) hydrogen bonds : angle 5.42278 ( 855) link_ALPHA1-3 : bond 0.02039 ( 1) link_ALPHA1-3 : angle 2.59677 ( 3) link_ALPHA1-6 : bond 0.01266 ( 2) link_ALPHA1-6 : angle 2.89517 ( 6) link_BETA1-2 : bond 0.00973 ( 1) link_BETA1-2 : angle 6.44162 ( 3) link_BETA1-4 : bond 0.01043 ( 12) link_BETA1-4 : angle 2.99727 ( 36) link_NAG-ASN : bond 0.00765 ( 11) link_NAG-ASN : angle 3.59968 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8172 (mt0) cc_final: 0.7772 (mm110) REVERT: A 525 ARG cc_start: 0.8594 (mpp-170) cc_final: 0.8272 (mpp80) REVERT: A 592 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7522 (t) REVERT: B 38 MET cc_start: -0.0070 (mpt) cc_final: -0.0393 (mmp) REVERT: B 86 LEU cc_start: 0.6847 (tp) cc_final: 0.5721 (pt) REVERT: B 334 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8180 (mtpp) REVERT: C 1373 ASP cc_start: 0.8987 (t0) cc_final: 0.8775 (t0) REVERT: C 1380 ASN cc_start: 0.8389 (t0) cc_final: 0.8054 (t0) outliers start: 23 outliers final: 16 residues processed: 62 average time/residue: 0.5567 time to fit residues: 37.4817 Evaluate side-chains 58 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 1365 HIS Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 0.0870 chunk 18 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.084308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.047174 restraints weight = 27274.766| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.36 r_work: 0.2696 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9996 Z= 0.121 Angle : 0.641 10.724 13631 Z= 0.291 Chirality : 0.047 0.402 1570 Planarity : 0.004 0.053 1742 Dihedral : 9.985 91.784 1881 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.22 % Allowed : 17.31 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.15 (0.23), residues: 1218 helix: 1.73 (0.47), residues: 120 sheet: 0.71 (0.25), residues: 411 loop : -0.98 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.012 0.001 TYR C1488 PHE 0.021 0.001 PHE A 569 TRP 0.008 0.001 TRP A 188 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9956) covalent geometry : angle 0.59024 (13524) SS BOND : bond 0.00107 ( 13) SS BOND : angle 0.43523 ( 26) hydrogen bonds : bond 0.03245 ( 314) hydrogen bonds : angle 5.24541 ( 855) link_ALPHA1-3 : bond 0.02341 ( 1) link_ALPHA1-3 : angle 2.96053 ( 3) link_ALPHA1-6 : bond 0.01284 ( 2) link_ALPHA1-6 : angle 2.84011 ( 6) link_BETA1-2 : bond 0.00984 ( 1) link_BETA1-2 : angle 6.22670 ( 3) link_BETA1-4 : bond 0.01057 ( 12) link_BETA1-4 : angle 2.95297 ( 36) link_NAG-ASN : bond 0.00673 ( 11) link_NAG-ASN : angle 3.39687 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8103 (mt0) cc_final: 0.7792 (mm110) REVERT: B 38 MET cc_start: -0.0166 (mpt) cc_final: -0.0450 (mmp) REVERT: B 86 LEU cc_start: 0.6884 (tp) cc_final: 0.5832 (pt) REVERT: C 1373 ASP cc_start: 0.8914 (t0) cc_final: 0.8700 (t0) REVERT: C 1380 ASN cc_start: 0.8336 (t0) cc_final: 0.7989 (t0) outliers start: 23 outliers final: 15 residues processed: 60 average time/residue: 0.4925 time to fit residues: 32.1717 Evaluate side-chains 55 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 1365 HIS Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.083682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046599 restraints weight = 27162.930| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.32 r_work: 0.2678 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9996 Z= 0.146 Angle : 0.658 11.380 13631 Z= 0.300 Chirality : 0.047 0.398 1570 Planarity : 0.004 0.053 1742 Dihedral : 9.779 89.161 1880 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.84 % Allowed : 17.99 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.11 (0.23), residues: 1218 helix: 2.01 (0.49), residues: 114 sheet: 0.72 (0.25), residues: 417 loop : -0.98 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.013 0.001 TYR C1488 PHE 0.019 0.001 PHE A 569 TRP 0.009 0.001 TRP A 188 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9956) covalent geometry : angle 0.60899 (13524) SS BOND : bond 0.00127 ( 13) SS BOND : angle 0.44943 ( 26) hydrogen bonds : bond 0.03657 ( 314) hydrogen bonds : angle 5.23952 ( 855) link_ALPHA1-3 : bond 0.02282 ( 1) link_ALPHA1-3 : angle 2.87330 ( 3) link_ALPHA1-6 : bond 0.01299 ( 2) link_ALPHA1-6 : angle 2.74995 ( 6) link_BETA1-2 : bond 0.00970 ( 1) link_BETA1-2 : angle 6.31609 ( 3) link_BETA1-4 : bond 0.00996 ( 12) link_BETA1-4 : angle 2.89695 ( 36) link_NAG-ASN : bond 0.00636 ( 11) link_NAG-ASN : angle 3.42659 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8243 (mt0) cc_final: 0.7928 (mm110) REVERT: A 409 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.9005 (t) REVERT: B 38 MET cc_start: 0.0004 (mpt) cc_final: -0.0293 (mmp) REVERT: B 86 LEU cc_start: 0.6903 (tp) cc_final: 0.5838 (pt) REVERT: C 1373 ASP cc_start: 0.8927 (t0) cc_final: 0.8485 (t0) REVERT: C 1380 ASN cc_start: 0.8352 (t0) cc_final: 0.8004 (t0) outliers start: 19 outliers final: 15 residues processed: 56 average time/residue: 0.5273 time to fit residues: 32.3262 Evaluate side-chains 54 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 1365 HIS Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.083575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046669 restraints weight = 27016.233| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.31 r_work: 0.2676 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9996 Z= 0.150 Angle : 0.658 11.832 13631 Z= 0.301 Chirality : 0.048 0.398 1570 Planarity : 0.004 0.053 1742 Dihedral : 9.500 86.040 1880 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.03 % Allowed : 18.09 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.12 (0.23), residues: 1218 helix: 1.95 (0.48), residues: 114 sheet: 0.72 (0.25), residues: 417 loop : -0.98 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.013 0.001 TYR C1488 PHE 0.015 0.001 PHE A 569 TRP 0.009 0.001 TRP A 188 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9956) covalent geometry : angle 0.60980 (13524) SS BOND : bond 0.00127 ( 13) SS BOND : angle 0.45163 ( 26) hydrogen bonds : bond 0.03630 ( 314) hydrogen bonds : angle 5.21514 ( 855) link_ALPHA1-3 : bond 0.02330 ( 1) link_ALPHA1-3 : angle 2.92770 ( 3) link_ALPHA1-6 : bond 0.01284 ( 2) link_ALPHA1-6 : angle 2.69661 ( 6) link_BETA1-2 : bond 0.00947 ( 1) link_BETA1-2 : angle 6.21027 ( 3) link_BETA1-4 : bond 0.00998 ( 12) link_BETA1-4 : angle 2.88377 ( 36) link_NAG-ASN : bond 0.00660 ( 11) link_NAG-ASN : angle 3.38209 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8384 (mt0) cc_final: 0.7953 (mm110) REVERT: A 409 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8981 (t) REVERT: A 592 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7553 (t) REVERT: B 38 MET cc_start: 0.0050 (mpt) cc_final: -0.0256 (mmp) REVERT: B 86 LEU cc_start: 0.7046 (tp) cc_final: 0.5887 (pt) REVERT: B 334 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8218 (mtmm) REVERT: C 1373 ASP cc_start: 0.8991 (t0) cc_final: 0.8566 (t0) REVERT: C 1380 ASN cc_start: 0.8366 (t0) cc_final: 0.8011 (t0) outliers start: 21 outliers final: 16 residues processed: 60 average time/residue: 0.5380 time to fit residues: 34.9376 Evaluate side-chains 57 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 1365 HIS Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.083636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046705 restraints weight = 27089.949| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.33 r_work: 0.2677 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9996 Z= 0.142 Angle : 0.662 11.951 13631 Z= 0.303 Chirality : 0.048 0.396 1570 Planarity : 0.004 0.053 1742 Dihedral : 9.314 84.050 1880 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.13 % Allowed : 17.79 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.13 (0.23), residues: 1218 helix: 1.97 (0.48), residues: 114 sheet: 0.72 (0.25), residues: 416 loop : -0.99 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.013 0.001 TYR C1488 PHE 0.018 0.001 PHE B 423 TRP 0.009 0.001 TRP A 188 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9956) covalent geometry : angle 0.61508 (13524) SS BOND : bond 0.00193 ( 13) SS BOND : angle 0.43274 ( 26) hydrogen bonds : bond 0.03564 ( 314) hydrogen bonds : angle 5.20107 ( 855) link_ALPHA1-3 : bond 0.02424 ( 1) link_ALPHA1-3 : angle 3.00229 ( 3) link_ALPHA1-6 : bond 0.01332 ( 2) link_ALPHA1-6 : angle 2.68829 ( 6) link_BETA1-2 : bond 0.00953 ( 1) link_BETA1-2 : angle 6.15486 ( 3) link_BETA1-4 : bond 0.00995 ( 12) link_BETA1-4 : angle 2.87746 ( 36) link_NAG-ASN : bond 0.00636 ( 11) link_NAG-ASN : angle 3.36945 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8401 (mt0) cc_final: 0.7975 (mm110) REVERT: A 409 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8982 (t) REVERT: A 592 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7605 (t) REVERT: B 38 MET cc_start: 0.0061 (mpt) cc_final: -0.0257 (mmp) REVERT: B 86 LEU cc_start: 0.7000 (tp) cc_final: 0.5900 (pt) REVERT: B 334 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8224 (mtmm) REVERT: C 1373 ASP cc_start: 0.8988 (t0) cc_final: 0.8563 (t0) REVERT: C 1380 ASN cc_start: 0.8374 (t0) cc_final: 0.8014 (t0) outliers start: 22 outliers final: 14 residues processed: 57 average time/residue: 0.5473 time to fit residues: 33.9635 Evaluate side-chains 55 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 481 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 1365 HIS Chi-restraints excluded: chain C residue 1416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.083090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.046121 restraints weight = 27185.624| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.32 r_work: 0.2660 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9996 Z= 0.167 Angle : 0.678 12.591 13631 Z= 0.312 Chirality : 0.048 0.393 1570 Planarity : 0.004 0.053 1742 Dihedral : 9.063 78.700 1880 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.84 % Allowed : 17.99 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.19 (0.23), residues: 1218 helix: 1.91 (0.48), residues: 114 sheet: 0.70 (0.26), residues: 403 loop : -1.01 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 426 TYR 0.014 0.001 TYR C1488 PHE 0.016 0.002 PHE B 423 TRP 0.008 0.001 TRP A 188 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9956) covalent geometry : angle 0.63132 (13524) SS BOND : bond 0.00169 ( 13) SS BOND : angle 0.47445 ( 26) hydrogen bonds : bond 0.03886 ( 314) hydrogen bonds : angle 5.24754 ( 855) link_ALPHA1-3 : bond 0.02387 ( 1) link_ALPHA1-3 : angle 2.94880 ( 3) link_ALPHA1-6 : bond 0.01331 ( 2) link_ALPHA1-6 : angle 2.64301 ( 6) link_BETA1-2 : bond 0.00926 ( 1) link_BETA1-2 : angle 6.13974 ( 3) link_BETA1-4 : bond 0.00964 ( 12) link_BETA1-4 : angle 2.90699 ( 36) link_NAG-ASN : bond 0.00670 ( 11) link_NAG-ASN : angle 3.44581 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.15 seconds wall clock time: 77 minutes 16.20 seconds (4636.20 seconds total)