Starting phenix.real_space_refine on Sun May 11 01:48:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tcf_41153/05_2025/8tcf_41153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tcf_41153/05_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_41153/05_2025/8tcf_41153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tcf_41153/05_2025/8tcf_41153.map" model { file = "/net/cci-nas-00/data/ceres_data/8tcf_41153/05_2025/8tcf_41153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tcf_41153/05_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-5687/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: 4.87, per 1000 atoms: 0.69 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: 1.87 Conformation dependent library (CDL) restraints added in 946.5 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: 0.80 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: 1.96 Time building geometry restraints manager: 2.17 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: 2.240 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- 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 : 0.772 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: 1.1708 time to fit residues: 220.7334 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 : 0.719 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120636 restraints weight = 9947.516| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.53 r_work: 0.3477 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 1.415 Fit side-chains REVERT: A 34 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: A 302 ASP cc_start: 0.7894 (t0) cc_final: 0.7652 (t0) REVERT: A 369 LYS cc_start: 0.7753 (mmpt) cc_final: 0.7152 (mtmt) REVERT: B 351 GLU cc_start: 0.7097 (mp0) cc_final: 0.6795 (mp0) REVERT: B 387 LEU cc_start: 0.6215 (mp) cc_final: 0.5975 (mm) REVERT: B 394 MET cc_start: 0.6116 (tpt) cc_final: 0.5663 (tpt) outliers start: 20 outliers final: 6 residues processed: 114 average time/residue: 1.1430 time to fit residues: 137.9816 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 : 0.708 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 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: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.139920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113006 restraints weight = 9907.631| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.50 r_work: 0.3390 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7223 Z= 0.184 Angle : 0.664 9.708 9822 Z= 0.338 Chirality : 0.049 0.261 1107 Planarity : 0.005 0.037 1260 Dihedral : 7.742 69.909 1273 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 3.25 % Allowed : 13.67 % Favored : 83.09 % 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: 0.31 (0.28), residues: 870 helix: -0.36 (0.44), residues: 134 sheet: 0.79 (0.28), residues: 304 loop : 0.08 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 179 HIS 0.007 0.002 HIS C 37 PHE 0.018 0.002 PHE A 276 TYR 0.023 0.002 TYR C 43 ARG 0.007 0.001 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00946 ( 8) link_NAG-ASN : angle 3.36195 ( 24) link_ALPHA1-6 : bond 0.01285 ( 1) link_ALPHA1-6 : angle 1.23263 ( 3) link_BETA1-4 : bond 0.01278 ( 5) link_BETA1-4 : angle 2.94027 ( 15) link_ALPHA1-2 : bond 0.00640 ( 1) link_ALPHA1-2 : angle 1.57209 ( 3) link_ALPHA1-3 : bond 0.01120 ( 1) link_ALPHA1-3 : angle 1.35566 ( 3) hydrogen bonds : bond 0.04289 ( 246) hydrogen bonds : angle 6.43497 ( 624) SS BOND : bond 0.00311 ( 9) SS BOND : angle 0.97474 ( 18) covalent geometry : bond 0.00425 ( 7198) covalent geometry : angle 0.63221 ( 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 111 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.724 Fit side-chains REVERT: B 193 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 271 VAL cc_start: 0.8567 (p) cc_final: 0.8266 (t) REVERT: B 374 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7326 (ttm) REVERT: B 394 MET cc_start: 0.6406 (tpt) cc_final: 0.5964 (tpt) REVERT: C 13 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8505 (mpp) outliers start: 24 outliers final: 13 residues processed: 102 average time/residue: 0.9970 time to fit residues: 108.3627 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 97 SER 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 B residue 92 ASN 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 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: 0.8980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114564 restraints weight = 9836.123| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.46 r_work: 0.3401 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7223 Z= 0.139 Angle : 0.607 10.295 9822 Z= 0.306 Chirality : 0.048 0.261 1107 Planarity : 0.004 0.040 1260 Dihedral : 7.231 64.692 1273 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 2.57 % Allowed : 15.16 % Favored : 82.27 % 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: 0.34 (0.28), residues: 870 helix: -0.25 (0.46), residues: 134 sheet: 0.98 (0.29), residues: 296 loop : -0.06 (0.29), residues: 440 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 0.015 0.001 PHE A 276 TYR 0.028 0.002 TYR C 43 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 8) link_NAG-ASN : angle 3.16955 ( 24) link_ALPHA1-6 : bond 0.01032 ( 1) link_ALPHA1-6 : angle 1.14269 ( 3) link_BETA1-4 : bond 0.01185 ( 5) link_BETA1-4 : angle 2.72013 ( 15) link_ALPHA1-2 : bond 0.00232 ( 1) link_ALPHA1-2 : angle 1.59590 ( 3) link_ALPHA1-3 : bond 0.01063 ( 1) link_ALPHA1-3 : angle 1.63708 ( 3) hydrogen bonds : bond 0.03624 ( 246) hydrogen bonds : angle 6.14216 ( 624) SS BOND : bond 0.00219 ( 9) SS BOND : angle 0.62237 ( 18) covalent geometry : bond 0.00313 ( 7198) covalent geometry : angle 0.57585 ( 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 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.800 Fit side-chains REVERT: A 369 LYS cc_start: 0.7815 (mmpt) cc_final: 0.7180 (mtpt) REVERT: B 204 ILE cc_start: 0.8139 (mt) cc_final: 0.7895 (tt) REVERT: B 271 VAL cc_start: 0.8584 (p) cc_final: 0.8266 (t) REVERT: B 374 MET cc_start: 0.7406 (ptp) cc_final: 0.7173 (ttm) REVERT: B 394 MET cc_start: 0.6238 (tpt) cc_final: 0.5821 (tpt) REVERT: C 13 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8500 (mpp) REVERT: C 41 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6570 (mm-30) REVERT: C 71 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7045 (mt-10) outliers start: 19 outliers final: 10 residues processed: 92 average time/residue: 0.9611 time to fit residues: 94.8380 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 136 THR 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: 3.9990 chunk 85 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.138491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110884 restraints weight = 9849.407| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.56 r_work: 0.3334 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7223 Z= 0.162 Angle : 0.615 9.129 9822 Z= 0.311 Chirality : 0.049 0.268 1107 Planarity : 0.004 0.037 1260 Dihedral : 7.145 61.646 1273 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 3.52 % Allowed : 14.88 % 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: 0.24 (0.28), residues: 870 helix: -0.34 (0.45), residues: 134 sheet: 0.98 (0.29), residues: 295 loop : -0.17 (0.29), residues: 441 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 0.028 0.002 TYR C 43 ARG 0.005 0.001 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.01110 ( 8) link_NAG-ASN : angle 3.07234 ( 24) link_ALPHA1-6 : bond 0.00972 ( 1) link_ALPHA1-6 : angle 1.19132 ( 3) link_BETA1-4 : bond 0.01217 ( 5) link_BETA1-4 : angle 2.70190 ( 15) link_ALPHA1-2 : bond 0.00344 ( 1) link_ALPHA1-2 : angle 1.50017 ( 3) link_ALPHA1-3 : bond 0.01121 ( 1) link_ALPHA1-3 : angle 1.65183 ( 3) hydrogen bonds : bond 0.03796 ( 246) hydrogen bonds : angle 6.06597 ( 624) SS BOND : bond 0.00227 ( 9) SS BOND : angle 0.57551 ( 18) covalent geometry : bond 0.00369 ( 7198) covalent geometry : angle 0.58683 ( 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 104 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.717 Fit side-chains REVERT: A 117 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: A 203 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7984 (tmmt) REVERT: A 369 LYS cc_start: 0.7780 (mmpt) cc_final: 0.7249 (mtpt) REVERT: B 133 ARG cc_start: 0.7857 (ptp-110) cc_final: 0.7572 (ptp-110) REVERT: B 204 ILE cc_start: 0.8180 (mt) cc_final: 0.7910 (tt) REVERT: B 394 MET cc_start: 0.6316 (tpt) cc_final: 0.5886 (tpt) REVERT: C 13 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8490 (mpp) REVERT: C 41 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6511 (mm-30) REVERT: C 71 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7167 (mt-10) outliers start: 26 outliers final: 13 residues processed: 94 average time/residue: 1.0012 time to fit residues: 100.3779 Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER 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 203 LYS 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 350 VAL Chi-restraints excluded: chain C residue 13 MET 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: 0.1980 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.139654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112622 restraints weight = 10023.840| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.56 r_work: 0.3343 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7223 Z= 0.137 Angle : 0.592 9.334 9822 Z= 0.299 Chirality : 0.048 0.261 1107 Planarity : 0.004 0.043 1260 Dihedral : 6.914 58.785 1273 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.01 % Rotamer: Outliers : 2.84 % Allowed : 15.02 % 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: 0.30 (0.28), residues: 870 helix: -0.19 (0.46), residues: 133 sheet: 1.02 (0.29), residues: 294 loop : -0.17 (0.30), residues: 443 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 0.014 0.001 PHE A 276 TYR 0.029 0.002 TYR C 43 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.01096 ( 8) link_NAG-ASN : angle 2.98555 ( 24) link_ALPHA1-6 : bond 0.01020 ( 1) link_ALPHA1-6 : angle 1.17635 ( 3) link_BETA1-4 : bond 0.01145 ( 5) link_BETA1-4 : angle 2.63468 ( 15) link_ALPHA1-2 : bond 0.00331 ( 1) link_ALPHA1-2 : angle 1.48393 ( 3) link_ALPHA1-3 : bond 0.01201 ( 1) link_ALPHA1-3 : angle 1.79969 ( 3) hydrogen bonds : bond 0.03507 ( 246) hydrogen bonds : angle 5.97149 ( 624) SS BOND : bond 0.00185 ( 9) SS BOND : angle 0.46847 ( 18) covalent geometry : bond 0.00308 ( 7198) covalent geometry : angle 0.56336 ( 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: 21 poor density : 79 time to evaluate : 0.725 Fit side-chains REVERT: A 117 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: A 203 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7944 (tmmt) REVERT: B 112 ASP cc_start: 0.8265 (t0) cc_final: 0.8057 (t0) REVERT: B 204 ILE cc_start: 0.8143 (mt) cc_final: 0.7868 (tt) REVERT: B 271 VAL cc_start: 0.8545 (p) cc_final: 0.8289 (t) REVERT: B 394 MET cc_start: 0.6308 (tpt) cc_final: 0.5888 (tpt) REVERT: C 41 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6385 (mm-30) REVERT: C 71 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7085 (mp0) outliers start: 21 outliers final: 12 residues processed: 90 average time/residue: 1.0762 time to fit residues: 102.9888 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER 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 203 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 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: 0.5980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 0.0010 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.139877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113077 restraints weight = 9832.192| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.53 r_work: 0.3350 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7223 Z= 0.128 Angle : 0.585 9.065 9822 Z= 0.294 Chirality : 0.047 0.256 1107 Planarity : 0.004 0.038 1260 Dihedral : 6.722 56.120 1273 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 15.29 % Favored : 82.41 % 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: 0.36 (0.29), residues: 870 helix: -0.13 (0.47), residues: 134 sheet: 1.07 (0.30), residues: 288 loop : -0.12 (0.30), residues: 448 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 0.012 0.001 PHE A 276 TYR 0.030 0.002 TYR C 43 ARG 0.004 0.000 ARG B 370 Details of bonding type rmsd link_NAG-ASN : bond 0.01120 ( 8) link_NAG-ASN : angle 2.87296 ( 24) link_ALPHA1-6 : bond 0.00946 ( 1) link_ALPHA1-6 : angle 1.18788 ( 3) link_BETA1-4 : bond 0.01280 ( 5) link_BETA1-4 : angle 2.61667 ( 15) link_ALPHA1-2 : bond 0.00318 ( 1) link_ALPHA1-2 : angle 1.44022 ( 3) link_ALPHA1-3 : bond 0.01123 ( 1) link_ALPHA1-3 : angle 1.86203 ( 3) hydrogen bonds : bond 0.03310 ( 246) hydrogen bonds : angle 5.81271 ( 624) SS BOND : bond 0.00181 ( 9) SS BOND : angle 0.44379 ( 18) covalent geometry : bond 0.00286 ( 7198) covalent geometry : angle 0.55832 ( 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 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.796 Fit side-chains REVERT: A 117 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8140 (mm-30) REVERT: A 148 ASP cc_start: 0.7968 (m-30) cc_final: 0.7291 (t70) REVERT: A 203 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8005 (tmmt) REVERT: A 369 LYS cc_start: 0.7794 (mmpt) cc_final: 0.7164 (mtmt) REVERT: B 133 ARG cc_start: 0.7996 (ptp-110) cc_final: 0.7078 (ppp-140) REVERT: B 204 ILE cc_start: 0.8074 (mt) cc_final: 0.7835 (tt) REVERT: B 271 VAL cc_start: 0.8474 (p) cc_final: 0.8205 (t) REVERT: B 370 ARG cc_start: 0.8205 (mmt180) cc_final: 0.7706 (mmt90) REVERT: B 394 MET cc_start: 0.6361 (tpt) cc_final: 0.5932 (tpt) REVERT: C 46 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8051 (t) REVERT: C 55 LYS cc_start: 0.7187 (mtmm) cc_final: 0.6724 (mptt) REVERT: C 71 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7079 (mp0) outliers start: 17 outliers final: 10 residues processed: 89 average time/residue: 1.0390 time to fit residues: 98.6924 Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER 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 203 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 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: 0.5980 chunk 40 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 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 = 0.3830 r_free = 0.3830 target = 0.140004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113546 restraints weight = 10004.068| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.53 r_work: 0.3352 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7223 Z= 0.131 Angle : 0.593 10.041 9822 Z= 0.298 Chirality : 0.047 0.255 1107 Planarity : 0.004 0.038 1260 Dihedral : 6.589 53.996 1273 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 2.30 % Allowed : 15.16 % Favored : 82.54 % 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: 0.34 (0.29), residues: 870 helix: -0.11 (0.47), residues: 134 sheet: 1.05 (0.30), residues: 289 loop : -0.14 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.012 0.001 PHE A 276 TYR 0.029 0.002 TYR C 43 ARG 0.004 0.000 ARG B 370 Details of bonding type rmsd link_NAG-ASN : bond 0.01108 ( 8) link_NAG-ASN : angle 2.81513 ( 24) link_ALPHA1-6 : bond 0.00927 ( 1) link_ALPHA1-6 : angle 1.20610 ( 3) link_BETA1-4 : bond 0.01165 ( 5) link_BETA1-4 : angle 2.58524 ( 15) link_ALPHA1-2 : bond 0.00328 ( 1) link_ALPHA1-2 : angle 1.43322 ( 3) link_ALPHA1-3 : bond 0.01112 ( 1) link_ALPHA1-3 : angle 1.89854 ( 3) hydrogen bonds : bond 0.03275 ( 246) hydrogen bonds : angle 5.78538 ( 624) SS BOND : bond 0.00141 ( 9) SS BOND : angle 0.49734 ( 18) covalent geometry : bond 0.00295 ( 7198) covalent geometry : angle 0.56697 ( 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.707 Fit side-chains REVERT: A 148 ASP cc_start: 0.7995 (m-30) cc_final: 0.7376 (t0) REVERT: A 203 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8042 (tmmt) REVERT: A 369 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7248 (mtpt) REVERT: B 133 ARG cc_start: 0.7962 (ptp-110) cc_final: 0.7079 (ppp-140) REVERT: B 204 ILE cc_start: 0.8117 (mt) cc_final: 0.7874 (tt) REVERT: B 271 VAL cc_start: 0.8473 (p) cc_final: 0.8230 (t) REVERT: B 370 ARG cc_start: 0.8146 (mmt180) cc_final: 0.7747 (mmt90) REVERT: B 394 MET cc_start: 0.6460 (tpt) cc_final: 0.6041 (tpt) REVERT: C 13 MET cc_start: 0.8568 (mtp) cc_final: 0.8273 (mtm) REVERT: C 71 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7071 (mp0) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 1.0138 time to fit residues: 93.1081 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER 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 203 LYS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 68 ILE 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: 0.6980 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 0.0010 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.139204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112551 restraints weight = 9997.778| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.54 r_work: 0.3339 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7223 Z= 0.142 Angle : 0.609 12.955 9822 Z= 0.305 Chirality : 0.048 0.255 1107 Planarity : 0.004 0.034 1260 Dihedral : 6.561 52.635 1273 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 1.76 % Allowed : 16.37 % 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: 0.40 (0.29), residues: 870 helix: 0.13 (0.48), residues: 126 sheet: 1.03 (0.30), residues: 288 loop : -0.12 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.010 0.001 HIS C 37 PHE 0.027 0.001 PHE B 93 TYR 0.017 0.002 TYR B 339 ARG 0.004 0.000 ARG C 6 Details of bonding type rmsd link_NAG-ASN : bond 0.01123 ( 8) link_NAG-ASN : angle 2.69766 ( 24) link_ALPHA1-6 : bond 0.00898 ( 1) link_ALPHA1-6 : angle 1.22921 ( 3) link_BETA1-4 : bond 0.01164 ( 5) link_BETA1-4 : angle 2.59588 ( 15) link_ALPHA1-2 : bond 0.00397 ( 1) link_ALPHA1-2 : angle 1.45412 ( 3) link_ALPHA1-3 : bond 0.01125 ( 1) link_ALPHA1-3 : angle 1.90747 ( 3) hydrogen bonds : bond 0.03342 ( 246) hydrogen bonds : angle 5.85647 ( 624) SS BOND : bond 0.00133 ( 9) SS BOND : angle 0.49495 ( 18) covalent geometry : bond 0.00325 ( 7198) covalent geometry : angle 0.58492 ( 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 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.835 Fit side-chains REVERT: A 148 ASP cc_start: 0.7941 (m-30) cc_final: 0.7285 (t70) REVERT: A 203 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8076 (tmmt) REVERT: A 369 LYS cc_start: 0.7820 (mmpt) cc_final: 0.7292 (mtmt) REVERT: B 133 ARG cc_start: 0.8013 (ptp-110) cc_final: 0.7100 (ppp-140) REVERT: B 204 ILE cc_start: 0.8140 (mt) cc_final: 0.7913 (tt) REVERT: B 271 VAL cc_start: 0.8452 (p) cc_final: 0.8205 (t) REVERT: B 370 ARG cc_start: 0.8173 (mmt180) cc_final: 0.7765 (mmt90) REVERT: B 394 MET cc_start: 0.6445 (tpt) cc_final: 0.6013 (tpt) REVERT: C 13 MET cc_start: 0.8587 (mtp) cc_final: 0.8269 (mtm) REVERT: C 55 LYS cc_start: 0.7250 (mtmm) cc_final: 0.6819 (mptt) REVERT: C 71 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7139 (mp0) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 1.0676 time to fit residues: 96.0357 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER 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 203 LYS Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 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: 0.5980 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 overall best weight: 0.7262 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.138839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111857 restraints weight = 10124.925| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.58 r_work: 0.3329 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.004 0.043 7223 Z= 0.154 Angle : 0.630 15.148 9822 Z= 0.317 Chirality : 0.048 0.253 1107 Planarity : 0.004 0.035 1260 Dihedral : 6.579 51.477 1273 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.76 % Allowed : 16.24 % 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: 0.31 (0.29), residues: 870 helix: 0.11 (0.48), residues: 126 sheet: 0.99 (0.30), residues: 279 loop : -0.19 (0.30), residues: 465 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 0.001 PHE B 93 TYR 0.033 0.002 TYR C 43 ARG 0.004 0.000 ARG C 6 Details of bonding type rmsd link_NAG-ASN : bond 0.01301 ( 8) link_NAG-ASN : angle 2.61365 ( 24) link_ALPHA1-6 : bond 0.00890 ( 1) link_ALPHA1-6 : angle 1.24408 ( 3) link_BETA1-4 : bond 0.01202 ( 5) link_BETA1-4 : angle 2.62133 ( 15) link_ALPHA1-2 : bond 0.00438 ( 1) link_ALPHA1-2 : angle 1.43497 ( 3) link_ALPHA1-3 : bond 0.01097 ( 1) link_ALPHA1-3 : angle 1.87879 ( 3) hydrogen bonds : bond 0.03437 ( 246) hydrogen bonds : angle 5.90922 ( 624) SS BOND : bond 0.00140 ( 9) SS BOND : angle 0.51221 ( 18) covalent geometry : bond 0.00356 ( 7198) covalent geometry : angle 0.60749 ( 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 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.715 Fit side-chains REVERT: A 148 ASP cc_start: 0.7986 (m-30) cc_final: 0.7332 (t70) REVERT: A 203 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8093 (tmmt) REVERT: A 369 LYS cc_start: 0.7863 (mmpt) cc_final: 0.7346 (mtmt) REVERT: B 86 ARG cc_start: 0.7463 (mtm110) cc_final: 0.6408 (ptp-170) REVERT: B 133 ARG cc_start: 0.8033 (ptp-110) cc_final: 0.7087 (ppp-140) REVERT: B 204 ILE cc_start: 0.8198 (mt) cc_final: 0.7964 (tt) REVERT: B 271 VAL cc_start: 0.8442 (p) cc_final: 0.8194 (t) REVERT: B 370 ARG cc_start: 0.8179 (mmt180) cc_final: 0.7783 (mmt90) REVERT: B 394 MET cc_start: 0.6488 (tpt) cc_final: 0.6089 (tpt) REVERT: C 13 MET cc_start: 0.8600 (mtp) cc_final: 0.8281 (mtm) REVERT: C 55 LYS cc_start: 0.7256 (mtmm) cc_final: 0.6883 (mptt) REVERT: C 70 VAL cc_start: 0.7824 (t) cc_final: 0.7575 (p) REVERT: C 71 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7163 (mp0) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 1.0381 time to fit residues: 93.0016 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 97 SER 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 203 LYS Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 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: 4.9990 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.0000 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.140193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113674 restraints weight = 9911.246| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.52 r_work: 0.3359 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7223 Z= 0.123 Angle : 0.596 13.886 9822 Z= 0.300 Chirality : 0.047 0.241 1107 Planarity : 0.004 0.035 1260 Dihedral : 6.360 49.048 1273 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.99 % Favored : 96.78 % Rotamer: Outliers : 1.49 % Allowed : 16.64 % 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: 0.42 (0.29), residues: 870 helix: 0.25 (0.49), residues: 126 sheet: 1.01 (0.30), residues: 288 loop : -0.12 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.008 0.001 HIS C 37 PHE 0.011 0.001 PHE A 19 TYR 0.014 0.001 TYR A 178 ARG 0.005 0.000 ARG A 33 Details of bonding type rmsd link_NAG-ASN : bond 0.01185 ( 8) link_NAG-ASN : angle 2.58624 ( 24) link_ALPHA1-6 : bond 0.00952 ( 1) link_ALPHA1-6 : angle 1.20716 ( 3) link_BETA1-4 : bond 0.01193 ( 5) link_BETA1-4 : angle 2.55669 ( 15) link_ALPHA1-2 : bond 0.00453 ( 1) link_ALPHA1-2 : angle 1.45266 ( 3) link_ALPHA1-3 : bond 0.01121 ( 1) link_ALPHA1-3 : angle 1.96598 ( 3) hydrogen bonds : bond 0.03143 ( 246) hydrogen bonds : angle 5.85921 ( 624) SS BOND : bond 0.00110 ( 9) SS BOND : angle 0.43063 ( 18) covalent geometry : bond 0.00277 ( 7198) covalent geometry : angle 0.57304 ( 9756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4865.75 seconds wall clock time: 84 minutes 42.75 seconds (5082.75 seconds total)