Starting phenix.real_space_refine on Mon Apr 28 08:30:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tcf_41153/04_2025/8tcf_41153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tcf_41153/04_2025/8tcf_41153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tcf_41153/04_2025/8tcf_41153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tcf_41153/04_2025/8tcf_41153.map" model { file = "/net/cci-nas-00/data/ceres_data/8tcf_41153/04_2025/8tcf_41153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tcf_41153/04_2025/8tcf_41153.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 35 5.16 5 C 4443 2.51 5 N 1179 2.21 5 O 1387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7050 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3406 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2823 Classifications: {'peptide': 359} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Chain: "C" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.66, per 1000 atoms: 0.66 Number of scatterers: 7050 At special positions: 0 Unit cell: (72.93, 98.736, 107.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 35 16.00 Mg 1 11.99 O 1387 8.00 N 1179 7.00 C 4443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.04 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.02 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.09 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 74 " distance=2.04 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 505 " - " ASN A 260 " " NAG B2003 " - " ASN B 191 " " NAG B2004 " - " ASN B 360 " " NAG B2005 " - " ASN B 379 " " NAG D 1 " - " ASN A 266 " " NAG E 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 389 " " NAG G 1 " - " ASN B 414 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 848.7 milliseconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 18.5% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 127 removed outlier: 4.007A pdb=" N SER B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'C' and resid 13 through 29 Processing helix chain 'C' and resid 51 through 63 removed outlier: 4.094A pdb=" N LYS C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.236A pdb=" N THR A 413 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 424 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLY A 411 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 426 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET A 409 " --> pdb=" O GLY A 426 " (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 79 through 81 removed outlier: 7.089A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.502A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101 removed outlier: 3.915A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.516A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.618A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.297A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.588A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB4, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.343A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 237 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 37 removed outlier: 3.870A pdb=" N ASN C 33 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL C 42 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N CYS C 3 " --> pdb=" O GLY C 48 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 624 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: 1.91 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1285 1.32 - 1.45: 1894 1.45 - 1.58: 3952 1.58 - 1.71: 15 1.71 - 1.84: 52 Bond restraints: 7198 Sorted by residual: bond pdb=" CA SER B 382 " pdb=" CB SER B 382 " ideal model delta sigma weight residual 1.527 1.474 0.054 1.49e-02 4.50e+03 1.29e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.456 -0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" CG PHE A 1 " pdb=" CD2 PHE A 1 " ideal model delta sigma weight residual 1.384 1.453 -0.069 2.10e-02 2.27e+03 1.08e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CG ASP B 209 " pdb=" OD2 ASP B 209 " ideal model delta sigma weight residual 1.249 1.188 0.061 1.90e-02 2.77e+03 1.04e+01 ... (remaining 7193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8112 1.70 - 3.41: 1327 3.41 - 5.11: 227 5.11 - 6.81: 73 6.81 - 8.52: 17 Bond angle restraints: 9756 Sorted by residual: angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 128.08 -8.52 1.02e+00 9.61e-01 6.97e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 127.97 -8.41 1.02e+00 9.61e-01 6.80e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.75 -8.19 1.02e+00 9.61e-01 6.45e+01 angle pdb=" C CYS A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 119.66 125.45 -5.79 7.30e-01 1.88e+00 6.28e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.02e+00 9.61e-01 6.02e+01 ... (remaining 9751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 4349 21.32 - 42.63: 104 42.63 - 63.95: 25 63.95 - 85.26: 16 85.26 - 106.58: 8 Dihedral angle restraints: 4502 sinusoidal: 1987 harmonic: 2515 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 33.56 59.44 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CD ARG B 378 " pdb=" NE ARG B 378 " pdb=" CZ ARG B 378 " pdb=" NH1 ARG B 378 " ideal model delta sinusoidal sigma weight residual 0.00 51.10 -51.10 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS B 397 " pdb=" SG CYS B 397 " pdb=" SG CYS B 425 " pdb=" CB CYS B 425 " ideal model delta sinusoidal sigma weight residual -86.00 -124.83 38.83 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 4499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 771 0.078 - 0.157: 256 0.157 - 0.235: 50 0.235 - 0.313: 15 0.313 - 0.392: 15 Chirality restraints: 1107 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.60e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.51e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.87e+01 ... (remaining 1104 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 378 " 0.863 9.50e-02 1.11e+02 3.87e-01 9.09e+01 pdb=" NE ARG B 378 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 378 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 378 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 378 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2005 " 0.079 2.00e-02 2.50e+03 6.51e-02 5.29e+01 pdb=" C7 NAG B2005 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG B2005 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG B2005 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG B2005 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2003 " 0.071 2.00e-02 2.50e+03 5.86e-02 4.29e+01 pdb=" C7 NAG B2003 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B2003 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG B2003 " -0.094 2.00e-02 2.50e+03 pdb=" O7 NAG B2003 " -0.011 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 29 2.42 - 3.04: 4416 3.04 - 3.66: 10012 3.66 - 4.28: 16815 4.28 - 4.90: 27099 Nonbonded interactions: 58371 Sorted by model distance: nonbonded pdb=" OD1 ASP C 12 " pdb="MG MG B2002 " model vdw 1.804 2.170 nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.809 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASP A 416 " pdb="CA CA A 503 " model vdw 2.093 2.510 nonbonded pdb=" OD1 ASP A 414 " pdb="CA CA A 503 " model vdw 2.097 2.510 ... (remaining 58366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.940 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.650 Find NCS groups from input model: 0.060 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:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.014 0.100 7223 Z= 0.755 Angle : 1.423 8.517 9822 Z= 0.950 Chirality : 0.090 0.392 1107 Planarity : 0.012 0.387 1260 Dihedral : 12.163 106.579 2869 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Rotamer: Outliers : 0.41 % Allowed : 0.95 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 870 helix: -0.59 (0.43), residues: 119 sheet: 0.85 (0.29), residues: 291 loop : 0.06 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.006 TRP B 230 HIS 0.007 0.001 HIS C 37 PHE 0.024 0.004 PHE A 276 TYR 0.034 0.006 TYR A 112 ARG 0.005 0.001 ARG B 378 Details of bonding type rmsd link_NAG-ASN : bond 0.06117 ( 8) link_NAG-ASN : angle 2.33756 ( 24) link_ALPHA1-6 : bond 0.05783 ( 1) link_ALPHA1-6 : angle 3.11538 ( 3) link_BETA1-4 : bond 0.06244 ( 5) link_BETA1-4 : angle 4.06100 ( 15) link_ALPHA1-2 : bond 0.07584 ( 1) link_ALPHA1-2 : angle 3.54006 ( 3) link_ALPHA1-3 : bond 0.08062 ( 1) link_ALPHA1-3 : angle 4.40716 ( 3) hydrogen bonds : bond 0.17124 ( 246) hydrogen bonds : angle 8.96783 ( 624) SS BOND : bond 0.02150 ( 9) SS BOND : angle 2.60416 ( 18) covalent geometry : bond 0.01391 ( 7198) covalent geometry : angle 1.40494 ( 9756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.788 Fit side-chains REVERT: A 162 ASP cc_start: 0.7276 (t0) cc_final: 0.6964 (t0) outliers start: 3 outliers final: 1 residues processed: 179 average time/residue: 1.2455 time to fit residues: 234.2792 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 381 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 320 GLN B 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120618 restraints weight = 9947.516| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.54 r_work: 0.3479 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7223 Z= 0.156 Angle : 0.692 9.443 9822 Z= 0.353 Chirality : 0.049 0.216 1107 Planarity : 0.005 0.040 1260 Dihedral : 8.298 81.661 1274 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.24 % Rotamer: Outliers : 2.71 % Allowed : 11.37 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 870 helix: -0.04 (0.46), residues: 126 sheet: 0.98 (0.28), residues: 296 loop : 0.10 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 93 HIS 0.010 0.001 HIS B 118 PHE 0.019 0.002 PHE A 276 TYR 0.021 0.002 TYR A 265 ARG 0.006 0.001 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.01293 ( 8) link_NAG-ASN : angle 3.33534 ( 24) link_ALPHA1-6 : bond 0.01533 ( 1) link_ALPHA1-6 : angle 1.56602 ( 3) link_BETA1-4 : bond 0.01355 ( 5) link_BETA1-4 : angle 3.22868 ( 15) link_ALPHA1-2 : bond 0.00350 ( 1) link_ALPHA1-2 : angle 1.79270 ( 3) link_ALPHA1-3 : bond 0.01295 ( 1) link_ALPHA1-3 : angle 1.06893 ( 3) hydrogen bonds : bond 0.04460 ( 246) hydrogen bonds : angle 6.91271 ( 624) SS BOND : bond 0.00439 ( 9) SS BOND : angle 0.96204 ( 18) covalent geometry : bond 0.00328 ( 7198) covalent geometry : angle 0.65984 ( 9756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.738 Fit side-chains REVERT: A 34 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: A 302 ASP cc_start: 0.7890 (t0) cc_final: 0.7646 (t0) REVERT: A 369 LYS cc_start: 0.7748 (mmpt) cc_final: 0.7148 (mtmt) REVERT: B 351 GLU cc_start: 0.7093 (mp0) cc_final: 0.6792 (mp0) REVERT: B 387 LEU cc_start: 0.6212 (mp) cc_final: 0.5973 (mm) REVERT: B 394 MET cc_start: 0.6113 (tpt) cc_final: 0.5659 (tpt) outliers start: 20 outliers final: 6 residues processed: 114 average time/residue: 1.4846 time to fit residues: 178.4001 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 68 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.0040 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.115917 restraints weight = 9917.382| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.48 r_work: 0.3418 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7223 Z= 0.156 Angle : 0.635 9.091 9822 Z= 0.324 Chirality : 0.048 0.256 1107 Planarity : 0.004 0.036 1260 Dihedral : 7.628 69.854 1273 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.24 % Rotamer: Outliers : 2.98 % Allowed : 13.80 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 870 helix: -0.24 (0.45), residues: 134 sheet: 0.84 (0.28), residues: 303 loop : 0.13 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.017 0.002 PHE A 276 TYR 0.026 0.002 TYR C 43 ARG 0.005 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00997 ( 8) link_NAG-ASN : angle 3.25752 ( 24) link_ALPHA1-6 : bond 0.01202 ( 1) link_ALPHA1-6 : angle 1.13930 ( 3) link_BETA1-4 : bond 0.01245 ( 5) link_BETA1-4 : angle 2.85949 ( 15) link_ALPHA1-2 : bond 0.00582 ( 1) link_ALPHA1-2 : angle 1.52486 ( 3) link_ALPHA1-3 : bond 0.01179 ( 1) link_ALPHA1-3 : angle 1.38276 ( 3) hydrogen bonds : bond 0.04082 ( 246) hydrogen bonds : angle 6.36657 ( 624) SS BOND : bond 0.00385 ( 9) SS BOND : angle 0.91974 ( 18) covalent geometry : bond 0.00350 ( 7198) covalent geometry : angle 0.60373 ( 9756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.768 Fit side-chains REVERT: B 374 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7293 (ttm) REVERT: B 394 MET cc_start: 0.6326 (tpt) cc_final: 0.5868 (tpt) REVERT: B 418 LYS cc_start: 0.7476 (mtpm) cc_final: 0.7114 (mmmt) REVERT: C 13 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8489 (mpp) outliers start: 22 outliers final: 11 residues processed: 101 average time/residue: 1.1584 time to fit residues: 124.7200 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.0060 chunk 5 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113725 restraints weight = 9869.854| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.45 r_work: 0.3391 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7223 Z= 0.157 Angle : 0.622 10.580 9822 Z= 0.314 Chirality : 0.048 0.265 1107 Planarity : 0.004 0.039 1260 Dihedral : 7.236 64.589 1273 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 2.57 % Allowed : 15.29 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 870 helix: -0.27 (0.46), residues: 134 sheet: 0.96 (0.29), residues: 298 loop : -0.06 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.016 0.002 PHE A 276 TYR 0.027 0.002 TYR C 43 ARG 0.006 0.001 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 8) link_NAG-ASN : angle 3.14152 ( 24) link_ALPHA1-6 : bond 0.00967 ( 1) link_ALPHA1-6 : angle 1.20023 ( 3) link_BETA1-4 : bond 0.01223 ( 5) link_BETA1-4 : angle 2.73346 ( 15) link_ALPHA1-2 : bond 0.00270 ( 1) link_ALPHA1-2 : angle 1.62446 ( 3) link_ALPHA1-3 : bond 0.01111 ( 1) link_ALPHA1-3 : angle 1.64629 ( 3) hydrogen bonds : bond 0.03756 ( 246) hydrogen bonds : angle 6.15122 ( 624) SS BOND : bond 0.00240 ( 9) SS BOND : angle 0.66647 ( 18) covalent geometry : bond 0.00358 ( 7198) covalent geometry : angle 0.59219 ( 9756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.756 Fit side-chains REVERT: A 369 LYS cc_start: 0.7887 (mmpt) cc_final: 0.7297 (mtpt) REVERT: B 204 ILE cc_start: 0.8151 (mt) cc_final: 0.7930 (tt) REVERT: B 271 VAL cc_start: 0.8545 (p) cc_final: 0.8254 (t) REVERT: B 374 MET cc_start: 0.7430 (ptp) cc_final: 0.7194 (ttm) REVERT: B 394 MET cc_start: 0.6242 (tpt) cc_final: 0.5743 (tpt) REVERT: C 13 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8468 (mpp) REVERT: C 41 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6588 (mm-30) REVERT: C 71 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7060 (mt-10) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 1.3134 time to fit residues: 129.5608 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112673 restraints weight = 9864.401| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.52 r_work: 0.3335 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7223 Z= 0.163 Angle : 0.620 9.511 9822 Z= 0.312 Chirality : 0.049 0.267 1107 Planarity : 0.004 0.037 1260 Dihedral : 7.138 61.566 1273 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 3.52 % Allowed : 14.34 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 870 helix: -0.35 (0.45), residues: 134 sheet: 0.99 (0.29), residues: 296 loop : -0.16 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.016 0.002 PHE A 276 TYR 0.029 0.002 TYR C 43 ARG 0.005 0.001 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00956 ( 8) link_NAG-ASN : angle 3.08212 ( 24) link_ALPHA1-6 : bond 0.01089 ( 1) link_ALPHA1-6 : angle 1.18714 ( 3) link_BETA1-4 : bond 0.01216 ( 5) link_BETA1-4 : angle 2.70425 ( 15) link_ALPHA1-2 : bond 0.00252 ( 1) link_ALPHA1-2 : angle 1.45554 ( 3) link_ALPHA1-3 : bond 0.01144 ( 1) link_ALPHA1-3 : angle 1.67171 ( 3) hydrogen bonds : bond 0.03802 ( 246) hydrogen bonds : angle 6.09541 ( 624) SS BOND : bond 0.00223 ( 9) SS BOND : angle 0.54747 ( 18) covalent geometry : bond 0.00371 ( 7198) covalent geometry : angle 0.59165 ( 9756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.234 Fit side-chains REVERT: A 117 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: A 369 LYS cc_start: 0.7780 (mmpt) cc_final: 0.7240 (mtpt) REVERT: B 133 ARG cc_start: 0.7842 (ptp-110) cc_final: 0.7529 (ptp-110) REVERT: B 196 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: B 204 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7915 (tt) REVERT: B 374 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7094 (ttm) REVERT: B 394 MET cc_start: 0.6307 (tpt) cc_final: 0.5879 (tpt) REVERT: C 13 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8520 (mpp) REVERT: C 41 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6464 (mm-30) REVERT: C 71 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7168 (mt-10) outliers start: 26 outliers final: 12 residues processed: 94 average time/residue: 1.3435 time to fit residues: 134.9459 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.139455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112600 restraints weight = 10007.383| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.54 r_work: 0.3338 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7223 Z= 0.145 Angle : 0.592 9.689 9822 Z= 0.300 Chirality : 0.048 0.261 1107 Planarity : 0.004 0.041 1260 Dihedral : 6.949 58.774 1273 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 2.98 % Allowed : 15.02 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 870 helix: -0.27 (0.46), residues: 134 sheet: 1.02 (0.29), residues: 294 loop : -0.18 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.014 0.001 PHE A 276 TYR 0.030 0.002 TYR C 43 ARG 0.003 0.000 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.01000 ( 8) link_NAG-ASN : angle 3.01654 ( 24) link_ALPHA1-6 : bond 0.00991 ( 1) link_ALPHA1-6 : angle 1.17811 ( 3) link_BETA1-4 : bond 0.01232 ( 5) link_BETA1-4 : angle 2.67504 ( 15) link_ALPHA1-2 : bond 0.00355 ( 1) link_ALPHA1-2 : angle 1.50438 ( 3) link_ALPHA1-3 : bond 0.01146 ( 1) link_ALPHA1-3 : angle 1.75641 ( 3) hydrogen bonds : bond 0.03542 ( 246) hydrogen bonds : angle 5.97453 ( 624) SS BOND : bond 0.00190 ( 9) SS BOND : angle 0.44928 ( 18) covalent geometry : bond 0.00329 ( 7198) covalent geometry : angle 0.56339 ( 9756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.065 Fit side-chains REVERT: A 117 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: B 112 ASP cc_start: 0.8183 (t0) cc_final: 0.7981 (t0) REVERT: B 204 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7887 (tt) REVERT: B 271 VAL cc_start: 0.8445 (p) cc_final: 0.8185 (t) REVERT: B 394 MET cc_start: 0.6300 (tpt) cc_final: 0.5873 (tpt) REVERT: C 55 LYS cc_start: 0.7228 (mtmm) cc_final: 0.6777 (mptt) REVERT: C 71 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7066 (mp0) outliers start: 22 outliers final: 10 residues processed: 89 average time/residue: 1.7823 time to fit residues: 168.6073 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 2 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113009 restraints weight = 9803.159| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.53 r_work: 0.3348 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7223 Z= 0.129 Angle : 0.588 8.773 9822 Z= 0.295 Chirality : 0.047 0.257 1107 Planarity : 0.004 0.039 1260 Dihedral : 6.730 56.133 1273 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 2.17 % Allowed : 15.83 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.29), residues: 870 helix: -0.15 (0.46), residues: 134 sheet: 1.10 (0.30), residues: 288 loop : -0.12 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.013 0.001 PHE A 276 TYR 0.030 0.002 TYR C 43 ARG 0.005 0.000 ARG B 370 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 8) link_NAG-ASN : angle 2.89566 ( 24) link_ALPHA1-6 : bond 0.00972 ( 1) link_ALPHA1-6 : angle 1.18776 ( 3) link_BETA1-4 : bond 0.01197 ( 5) link_BETA1-4 : angle 2.61751 ( 15) link_ALPHA1-2 : bond 0.00370 ( 1) link_ALPHA1-2 : angle 1.46000 ( 3) link_ALPHA1-3 : bond 0.01142 ( 1) link_ALPHA1-3 : angle 1.85116 ( 3) hydrogen bonds : bond 0.03352 ( 246) hydrogen bonds : angle 5.79821 ( 624) SS BOND : bond 0.00186 ( 9) SS BOND : angle 0.46420 ( 18) covalent geometry : bond 0.00292 ( 7198) covalent geometry : angle 0.56049 ( 9756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.059 Fit side-chains REVERT: A 148 ASP cc_start: 0.7976 (m-30) cc_final: 0.7293 (t70) REVERT: A 203 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7952 (tmmt) REVERT: A 369 LYS cc_start: 0.7831 (mmpt) cc_final: 0.7184 (mtmt) REVERT: B 86 ARG cc_start: 0.7370 (mtm110) cc_final: 0.6328 (ptp-170) REVERT: B 133 ARG cc_start: 0.8041 (ptp-110) cc_final: 0.7106 (ppp-140) REVERT: B 204 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7873 (tt) REVERT: B 271 VAL cc_start: 0.8462 (p) cc_final: 0.8203 (t) REVERT: B 370 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7765 (mmt90) REVERT: B 394 MET cc_start: 0.6335 (tpt) cc_final: 0.5900 (tpt) REVERT: C 46 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8042 (t) REVERT: C 71 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7096 (mp0) outliers start: 16 outliers final: 10 residues processed: 89 average time/residue: 1.5930 time to fit residues: 152.7302 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111937 restraints weight = 10005.275| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.54 r_work: 0.3331 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7223 Z= 0.153 Angle : 0.614 9.355 9822 Z= 0.309 Chirality : 0.048 0.258 1107 Planarity : 0.004 0.039 1260 Dihedral : 6.716 54.769 1273 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Rotamer: Outliers : 2.17 % Allowed : 15.97 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 870 helix: -0.20 (0.46), residues: 134 sheet: 1.07 (0.30), residues: 280 loop : -0.21 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.015 0.001 PHE A 276 TYR 0.029 0.002 TYR C 43 ARG 0.005 0.000 ARG A 33 Details of bonding type rmsd link_NAG-ASN : bond 0.01179 ( 8) link_NAG-ASN : angle 2.87987 ( 24) link_ALPHA1-6 : bond 0.00888 ( 1) link_ALPHA1-6 : angle 1.23425 ( 3) link_BETA1-4 : bond 0.01180 ( 5) link_BETA1-4 : angle 2.63519 ( 15) link_ALPHA1-2 : bond 0.00391 ( 1) link_ALPHA1-2 : angle 1.45480 ( 3) link_ALPHA1-3 : bond 0.01143 ( 1) link_ALPHA1-3 : angle 1.83176 ( 3) hydrogen bonds : bond 0.03472 ( 246) hydrogen bonds : angle 5.85673 ( 624) SS BOND : bond 0.00157 ( 9) SS BOND : angle 0.52647 ( 18) covalent geometry : bond 0.00351 ( 7198) covalent geometry : angle 0.58819 ( 9756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.766 Fit side-chains REVERT: A 148 ASP cc_start: 0.8023 (m-30) cc_final: 0.7355 (t70) REVERT: A 203 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7989 (tmmt) REVERT: A 369 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7298 (mtmt) REVERT: B 133 ARG cc_start: 0.7969 (ptp-110) cc_final: 0.7080 (ppp-140) REVERT: B 204 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7907 (tt) REVERT: B 271 VAL cc_start: 0.8440 (p) cc_final: 0.8194 (t) REVERT: B 370 ARG cc_start: 0.8201 (mmt180) cc_final: 0.7793 (mmt90) REVERT: B 394 MET cc_start: 0.6437 (tpt) cc_final: 0.6009 (tpt) REVERT: C 13 MET cc_start: 0.8596 (mtp) cc_final: 0.8221 (mtm) REVERT: C 46 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8068 (t) REVERT: C 55 LYS cc_start: 0.7196 (mtmm) cc_final: 0.6659 (mptt) REVERT: C 71 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7137 (mp0) outliers start: 16 outliers final: 12 residues processed: 85 average time/residue: 1.1094 time to fit residues: 101.2019 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111611 restraints weight = 10002.252| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.54 r_work: 0.3325 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7223 Z= 0.158 Angle : 0.625 13.232 9822 Z= 0.314 Chirality : 0.048 0.256 1107 Planarity : 0.004 0.036 1260 Dihedral : 6.699 53.576 1273 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 2.03 % Allowed : 16.37 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 870 helix: -0.21 (0.46), residues: 134 sheet: 1.03 (0.30), residues: 279 loop : -0.24 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.026 0.002 PHE B 93 TYR 0.017 0.002 TYR A 178 ARG 0.007 0.000 ARG A 33 Details of bonding type rmsd link_NAG-ASN : bond 0.01162 ( 8) link_NAG-ASN : angle 2.79039 ( 24) link_ALPHA1-6 : bond 0.00954 ( 1) link_ALPHA1-6 : angle 1.24063 ( 3) link_BETA1-4 : bond 0.01199 ( 5) link_BETA1-4 : angle 2.65475 ( 15) link_ALPHA1-2 : bond 0.00449 ( 1) link_ALPHA1-2 : angle 1.45357 ( 3) link_ALPHA1-3 : bond 0.01128 ( 1) link_ALPHA1-3 : angle 1.82761 ( 3) hydrogen bonds : bond 0.03492 ( 246) hydrogen bonds : angle 5.92224 ( 624) SS BOND : bond 0.00144 ( 9) SS BOND : angle 0.50690 ( 18) covalent geometry : bond 0.00363 ( 7198) covalent geometry : angle 0.60102 ( 9756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.760 Fit side-chains REVERT: A 148 ASP cc_start: 0.7984 (m-30) cc_final: 0.7313 (t70) REVERT: A 203 LYS cc_start: 0.8268 (ttpp) cc_final: 0.8008 (tmmt) REVERT: A 369 LYS cc_start: 0.7878 (mmpt) cc_final: 0.7321 (mtmt) REVERT: B 133 ARG cc_start: 0.7996 (ptp-110) cc_final: 0.7061 (ppp-140) REVERT: B 204 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7914 (tt) REVERT: B 271 VAL cc_start: 0.8444 (p) cc_final: 0.8194 (t) REVERT: B 370 ARG cc_start: 0.8203 (mmt180) cc_final: 0.7810 (mmt90) REVERT: B 394 MET cc_start: 0.6446 (tpt) cc_final: 0.6043 (tpt) REVERT: C 13 MET cc_start: 0.8613 (mtp) cc_final: 0.8317 (mtm) REVERT: C 46 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8076 (t) REVERT: C 55 LYS cc_start: 0.7207 (mtmm) cc_final: 0.6839 (mptt) REVERT: C 71 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7232 (mp0) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 1.0826 time to fit residues: 93.5747 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.138921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112262 restraints weight = 10133.486| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.55 r_work: 0.3338 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7223 Z= 0.141 Angle : 0.620 15.517 9822 Z= 0.311 Chirality : 0.048 0.250 1107 Planarity : 0.004 0.035 1260 Dihedral : 6.595 51.795 1273 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 2.30 % Allowed : 16.10 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 870 helix: -0.15 (0.46), residues: 134 sheet: 1.00 (0.30), residues: 279 loop : -0.24 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.028 0.001 PHE B 93 TYR 0.031 0.002 TYR C 43 ARG 0.003 0.000 ARG C 6 Details of bonding type rmsd link_NAG-ASN : bond 0.01248 ( 8) link_NAG-ASN : angle 2.57840 ( 24) link_ALPHA1-6 : bond 0.00910 ( 1) link_ALPHA1-6 : angle 1.22733 ( 3) link_BETA1-4 : bond 0.01191 ( 5) link_BETA1-4 : angle 2.64534 ( 15) link_ALPHA1-2 : bond 0.00446 ( 1) link_ALPHA1-2 : angle 1.42391 ( 3) link_ALPHA1-3 : bond 0.01136 ( 1) link_ALPHA1-3 : angle 1.88436 ( 3) hydrogen bonds : bond 0.03355 ( 246) hydrogen bonds : angle 5.90995 ( 624) SS BOND : bond 0.00134 ( 9) SS BOND : angle 0.48228 ( 18) covalent geometry : bond 0.00321 ( 7198) covalent geometry : angle 0.59797 ( 9756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.715 Fit side-chains REVERT: A 101 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7694 (tptm) REVERT: A 103 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: A 148 ASP cc_start: 0.7975 (m-30) cc_final: 0.7315 (t70) REVERT: A 203 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8034 (tmmt) REVERT: A 369 LYS cc_start: 0.7864 (mmpt) cc_final: 0.7351 (mtmt) REVERT: B 86 ARG cc_start: 0.7456 (mtm110) cc_final: 0.6401 (ptp-170) REVERT: B 133 ARG cc_start: 0.8017 (ptp-110) cc_final: 0.7064 (ppp-140) REVERT: B 204 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7893 (tt) REVERT: B 271 VAL cc_start: 0.8448 (p) cc_final: 0.8201 (t) REVERT: B 370 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7765 (mmt90) REVERT: B 394 MET cc_start: 0.6472 (tpt) cc_final: 0.6070 (tpt) REVERT: C 13 MET cc_start: 0.8589 (mtp) cc_final: 0.8255 (mtm) REVERT: C 41 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6387 (mm-30) REVERT: C 46 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8073 (t) REVERT: C 55 LYS cc_start: 0.7288 (mtmm) cc_final: 0.6914 (mptt) REVERT: C 71 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7243 (mp0) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 1.0364 time to fit residues: 97.3240 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 48 optimal weight: 0.0000 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113893 restraints weight = 9909.324| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.52 r_work: 0.3366 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7223 Z= 0.119 Angle : 0.578 8.648 9822 Z= 0.294 Chirality : 0.047 0.238 1107 Planarity : 0.004 0.034 1260 Dihedral : 6.323 48.682 1273 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % Rotamer: Outliers : 1.62 % Allowed : 16.78 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 870 helix: 0.27 (0.49), residues: 126 sheet: 1.06 (0.30), residues: 289 loop : -0.11 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 PHE 0.011 0.001 PHE A 276 TYR 0.014 0.001 TYR A 178 ARG 0.004 0.000 ARG C 6 Details of bonding type rmsd link_NAG-ASN : bond 0.01206 ( 8) link_NAG-ASN : angle 2.60576 ( 24) link_ALPHA1-6 : bond 0.00936 ( 1) link_ALPHA1-6 : angle 1.21248 ( 3) link_BETA1-4 : bond 0.01190 ( 5) link_BETA1-4 : angle 2.53217 ( 15) link_ALPHA1-2 : bond 0.00445 ( 1) link_ALPHA1-2 : angle 1.47613 ( 3) link_ALPHA1-3 : bond 0.01125 ( 1) link_ALPHA1-3 : angle 1.99640 ( 3) hydrogen bonds : bond 0.03100 ( 246) hydrogen bonds : angle 5.85849 ( 624) SS BOND : bond 0.00118 ( 9) SS BOND : angle 0.42349 ( 18) covalent geometry : bond 0.00263 ( 7198) covalent geometry : angle 0.55381 ( 9756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5940.60 seconds wall clock time: 107 minutes 7.26 seconds (6427.26 seconds total)