Starting phenix.real_space_refine on Thu Jul 2 06:31:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_41153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_41153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_41153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_41153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_41153.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_41153.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tcf_41153/07_2026/8tcf_41153.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 1.51, per 1000 atoms: 0.21 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: 0.62 Conformation dependent library (CDL) restraints added in 375.6 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: 0.17 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: 0.74 Time building geometry restraints manager: 0.82 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 - 17.99: 4013 17.99 - 35.98: 111 35.98 - 53.96: 27 53.96 - 71.95: 16 71.95 - 89.94: 7 Dihedral angle restraints: 4174 sinusoidal: 1659 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 4171 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: 3.840 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 11.125 89.939 2541 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), 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 ARG 0.005 0.001 ARG B 378 TYR 0.034 0.006 TYR A 112 PHE 0.024 0.004 PHE A 276 TRP 0.023 0.006 TRP B 230 HIS 0.007 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.01391 / 0.74 ( 7198) covalent geometry : angle 1.40494 / 0.95 ( 9756) SS BOND : bond 0.02150 / 1.02 ( 9) SS BOND : angle 2.60416 / 1.68 ( 18) hydrogen bonds : bond 0.17124 / 10.75 ( 246) hydrogen bonds : angle 8.96783 / 6.13 ( 624) link_ALPHA1-2 : bond 0.07584 / 3.99 ( 1) link_ALPHA1-2 : angle 3.54006 / 1.91 ( 3) link_ALPHA1-3 : bond 0.08062 / 4.24 ( 1) link_ALPHA1-3 : angle 4.40716 / 2.64 ( 3) link_ALPHA1-6 : bond 0.05783 / 3.04 ( 1) link_ALPHA1-6 : angle 3.11538 / 1.76 ( 3) link_BETA1-4 : bond 0.06244 / 3.54 ( 5) link_BETA1-4 : angle 4.06100 / 2.36 ( 15) link_NAG-ASN : bond 0.06117 / 3.36 ( 8) link_NAG-ASN : angle 2.33756 / 1.65 ( 24) *********************** 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 : 0.263 Fit side-chains REVERT: A 162 ASP cc_start: 0.7276 (t0) cc_final: 0.6963 (t0) outliers start: 3 outliers final: 1 residues processed: 179 average time/residue: 0.4661 time to fit residues: 87.9313 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 : 0.156 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN A 320 GLN B 161 HIS B 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119277 restraints weight = 9997.898| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.50 r_work: 0.3446 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7223 Z= 0.179 Angle : 0.707 8.890 9822 Z= 0.364 Chirality : 0.049 0.179 1107 Planarity : 0.005 0.052 1260 Dihedral : 4.963 22.864 946 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 2.71 % Allowed : 11.91 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.27), residues: 870 helix: -0.09 (0.46), residues: 127 sheet: 0.99 (0.28), residues: 296 loop : 0.14 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 248 TYR 0.021 0.002 TYR A 112 PHE 0.021 0.002 PHE A 276 TRP 0.013 0.002 TRP A 93 HIS 0.009 0.002 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 7198) covalent geometry : angle 0.67585 / 0.36 ( 9756) SS BOND : bond 0.00205 / 0.10 ( 9) SS BOND : angle 1.05393 / 0.63 ( 18) hydrogen bonds : bond 0.04884 / 3.12 ( 246) hydrogen bonds : angle 7.00137 / 4.82 ( 624) link_ALPHA1-2 : bond 0.00658 / 0.35 ( 1) link_ALPHA1-2 : angle 1.63159 / 1.26 ( 3) link_ALPHA1-3 : bond 0.01426 / 0.75 ( 1) link_ALPHA1-3 : angle 2.36640 / 1.44 ( 3) link_ALPHA1-6 : bond 0.00678 / 0.36 ( 1) link_ALPHA1-6 : angle 1.71614 / 1.59 ( 3) link_BETA1-4 : bond 0.01447 / 0.71 ( 5) link_BETA1-4 : angle 3.17632 / 1.93 ( 15) link_NAG-ASN : bond 0.01480 / 0.71 ( 8) link_NAG-ASN : angle 3.25941 / 2.39 ( 24) *********************** 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 115 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.256 Fit side-chains REVERT: A 34 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7947 (mtt) REVERT: A 369 LYS cc_start: 0.7849 (mmpt) cc_final: 0.7260 (mtpt) REVERT: B 137 PHE cc_start: 0.8472 (m-10) cc_final: 0.8208 (m-80) REVERT: B 370 ARG cc_start: 0.7978 (mpt90) cc_final: 0.7714 (mpt90) REVERT: B 387 LEU cc_start: 0.6230 (mp) cc_final: 0.5958 (mm) REVERT: B 394 MET cc_start: 0.6070 (tpt) cc_final: 0.5647 (tpt) REVERT: C 71 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7042 (mt-10) outliers start: 20 outliers final: 7 residues processed: 109 average time/residue: 0.4495 time to fit residues: 51.8065 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 415 ILE 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 46 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 206 ASN B 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.143661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117259 restraints weight = 9843.105| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.47 r_work: 0.3434 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3151 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= 0.138 Angle : 0.614 9.520 9822 Z= 0.312 Chirality : 0.047 0.148 1107 Planarity : 0.004 0.038 1260 Dihedral : 4.614 21.138 945 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 2.57 % Allowed : 13.67 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.28), residues: 870 helix: -0.19 (0.45), residues: 134 sheet: 0.90 (0.28), residues: 303 loop : 0.15 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 248 TYR 0.016 0.002 TYR A 265 PHE 0.015 0.002 PHE A 276 TRP 0.009 0.001 TRP C 60 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7198) covalent geometry : angle 0.58234 / 0.31 ( 9756) SS BOND : bond 0.00231 / 0.15 ( 9) SS BOND : angle 0.71123 / 0.43 ( 18) hydrogen bonds : bond 0.03897 / 2.48 ( 246) hydrogen bonds : angle 6.40440 / 4.37 ( 624) link_ALPHA1-2 : bond 0.00416 / 0.22 ( 1) link_ALPHA1-2 : angle 1.68756 / 1.06 ( 3) link_ALPHA1-3 : bond 0.00820 / 0.43 ( 1) link_ALPHA1-3 : angle 1.60810 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00666 / 0.35 ( 1) link_ALPHA1-6 : angle 1.22169 / 1.05 ( 3) link_BETA1-4 : bond 0.01295 / 0.63 ( 5) link_BETA1-4 : angle 2.74884 / 1.65 ( 15) link_NAG-ASN : bond 0.01065 / 0.51 ( 8) link_NAG-ASN : angle 3.22963 / 2.34 ( 24) *********************** 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 106 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 374 MET cc_start: 0.7533 (ptp) cc_final: 0.7266 (ttm) REVERT: B 394 MET cc_start: 0.6145 (tpt) cc_final: 0.5721 (tpt) REVERT: C 13 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (mpp) REVERT: C 71 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7031 (mt-10) outliers start: 19 outliers final: 8 residues processed: 99 average time/residue: 0.4514 time to fit residues: 47.4132 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 415 ILE 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 13 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111689 restraints weight = 9828.988| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.43 r_work: 0.3357 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7223 Z= 0.208 Angle : 0.675 9.320 9822 Z= 0.342 Chirality : 0.050 0.169 1107 Planarity : 0.005 0.038 1260 Dihedral : 4.803 20.442 945 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 3.38 % Allowed : 14.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.28), residues: 870 helix: -0.51 (0.44), residues: 134 sheet: 0.95 (0.29), residues: 297 loop : -0.07 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 437 TYR 0.024 0.002 TYR A 254 PHE 0.017 0.002 PHE A 163 TRP 0.009 0.002 TRP A 179 HIS 0.007 0.002 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 7198) covalent geometry : angle 0.64625 / 0.34 ( 9756) SS BOND : bond 0.00282 / 0.19 ( 9) SS BOND : angle 0.65146 / 0.42 ( 18) hydrogen bonds : bond 0.04243 / 2.67 ( 246) hydrogen bonds : angle 6.35626 / 4.39 ( 624) link_ALPHA1-2 : bond 0.00265 / 0.14 ( 1) link_ALPHA1-2 : angle 1.70936 / 1.11 ( 3) link_ALPHA1-3 : bond 0.00791 / 0.42 ( 1) link_ALPHA1-3 : angle 1.64938 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00444 / 0.23 ( 1) link_ALPHA1-6 : angle 1.46786 / 1.37 ( 3) link_BETA1-4 : bond 0.01219 / 0.58 ( 5) link_BETA1-4 : angle 2.76892 / 1.68 ( 15) link_NAG-ASN : bond 0.00798 / 0.38 ( 8) link_NAG-ASN : angle 3.25483 / 2.40 ( 24) *********************** 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 105 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7951 (mtp180) REVERT: A 216 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 275 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: A 369 LYS cc_start: 0.7899 (mmpt) cc_final: 0.7308 (mtmt) REVERT: B 204 ILE cc_start: 0.8168 (mt) cc_final: 0.7915 (tt) REVERT: B 374 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7272 (ttm) REVERT: B 394 MET cc_start: 0.6321 (tpt) cc_final: 0.5933 (tpt) REVERT: C 13 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8515 (mpp) REVERT: C 71 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7141 (mt-10) outliers start: 25 outliers final: 12 residues processed: 96 average time/residue: 0.4253 time to fit residues: 43.4377 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 136 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 226 SER 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 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.0050 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112221 restraints weight = 9868.017| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.56 r_work: 0.3352 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7223 Z= 0.128 Angle : 0.591 9.923 9822 Z= 0.299 Chirality : 0.047 0.160 1107 Planarity : 0.004 0.039 1260 Dihedral : 4.541 19.535 945 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.24 % Rotamer: Outliers : 2.71 % Allowed : 14.61 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.28), residues: 870 helix: -0.24 (0.46), residues: 134 sheet: 1.02 (0.29), residues: 296 loop : -0.15 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.025 0.002 TYR C 43 PHE 0.012 0.001 PHE A 276 TRP 0.007 0.001 TRP C 60 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7198) covalent geometry : angle 0.56127 / 0.29 ( 9756) SS BOND : bond 0.00184 / 0.13 ( 9) SS BOND : angle 0.43650 / 0.28 ( 18) hydrogen bonds : bond 0.03540 / 2.23 ( 246) hydrogen bonds : angle 6.11724 / 4.20 ( 624) link_ALPHA1-2 : bond 0.00202 / 0.11 ( 1) link_ALPHA1-2 : angle 1.80391 / 1.16 ( 3) link_ALPHA1-3 : bond 0.00656 / 0.35 ( 1) link_ALPHA1-3 : angle 1.37468 / 0.84 ( 3) link_ALPHA1-6 : bond 0.00560 / 0.29 ( 1) link_ALPHA1-6 : angle 1.24376 / 1.10 ( 3) link_BETA1-4 : bond 0.01221 / 0.59 ( 5) link_BETA1-4 : angle 2.56724 / 1.54 ( 15) link_NAG-ASN : bond 0.01109 / 0.53 ( 8) link_NAG-ASN : angle 3.12584 / 2.32 ( 24) *********************** 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 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.230 Fit side-chains REVERT: A 117 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: A 186 ASP cc_start: 0.7930 (t70) cc_final: 0.7535 (m-30) REVERT: A 275 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: A 369 LYS cc_start: 0.7792 (mmpt) cc_final: 0.7237 (mtpt) REVERT: B 112 ASP cc_start: 0.8192 (t0) cc_final: 0.7988 (t0) REVERT: B 133 ARG cc_start: 0.7950 (ptp-110) cc_final: 0.7682 (ptp-110) REVERT: B 204 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7902 (tt) REVERT: B 271 VAL cc_start: 0.8552 (p) cc_final: 0.8295 (t) REVERT: B 374 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7198 (ttm) REVERT: B 394 MET cc_start: 0.6258 (tpt) cc_final: 0.5839 (tpt) REVERT: C 6 ARG cc_start: 0.7901 (ttt90) cc_final: 0.7426 (ttt180) REVERT: C 13 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8518 (mpp) REVERT: C 71 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7050 (mp0) outliers start: 20 outliers final: 8 residues processed: 91 average time/residue: 0.4486 time to fit residues: 43.2319 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 308 LYS 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 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 45 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.139600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112581 restraints weight = 9997.221| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.54 r_work: 0.3334 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 0.038 7223 Z= 0.147 Angle : 0.595 9.137 9822 Z= 0.301 Chirality : 0.047 0.164 1107 Planarity : 0.004 0.041 1260 Dihedral : 4.485 18.946 945 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 2.71 % Allowed : 14.61 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.28), residues: 870 helix: -0.20 (0.46), residues: 133 sheet: 1.04 (0.29), residues: 289 loop : -0.17 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 248 TYR 0.031 0.002 TYR C 43 PHE 0.013 0.001 PHE A 19 TRP 0.008 0.001 TRP A 179 HIS 0.008 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7198) covalent geometry : angle 0.56751 / 0.30 ( 9756) SS BOND : bond 0.00187 / 0.13 ( 9) SS BOND : angle 0.44904 / 0.28 ( 18) hydrogen bonds : bond 0.03547 / 2.23 ( 246) hydrogen bonds : angle 5.96864 / 4.11 ( 624) link_ALPHA1-2 : bond 0.00160 / 0.08 ( 1) link_ALPHA1-2 : angle 1.90451 / 1.25 ( 3) link_ALPHA1-3 : bond 0.00656 / 0.35 ( 1) link_ALPHA1-3 : angle 1.30964 / 0.82 ( 3) link_ALPHA1-6 : bond 0.00499 / 0.26 ( 1) link_ALPHA1-6 : angle 1.34527 / 1.22 ( 3) link_BETA1-4 : bond 0.01183 / 0.57 ( 5) link_BETA1-4 : angle 2.50379 / 1.51 ( 15) link_NAG-ASN : bond 0.01105 / 0.53 ( 8) link_NAG-ASN : angle 2.98244 / 2.22 ( 24) *********************** 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 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: A 186 ASP cc_start: 0.7933 (t70) cc_final: 0.7500 (m-30) REVERT: A 216 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 275 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 112 ASP cc_start: 0.8158 (t0) cc_final: 0.7937 (t0) REVERT: B 204 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 271 VAL cc_start: 0.8404 (p) cc_final: 0.8133 (t) REVERT: B 394 MET cc_start: 0.6348 (tpt) cc_final: 0.5934 (tpt) REVERT: C 13 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8450 (mpp) REVERT: C 55 LYS cc_start: 0.7206 (mtmm) cc_final: 0.6757 (mptt) REVERT: C 71 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7086 (mp0) outliers start: 20 outliers final: 9 residues processed: 88 average time/residue: 0.4330 time to fit residues: 40.7856 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 275 TYR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.0040 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112691 restraints weight = 9966.899| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.54 r_work: 0.3339 rms_B_bonded: 2.90 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: 0.7967 moved from start: 0.4063 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= 0.139 Angle : 0.597 9.429 9822 Z= 0.300 Chirality : 0.047 0.164 1107 Planarity : 0.004 0.040 1260 Dihedral : 4.434 18.381 945 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.28), residues: 870 helix: -0.17 (0.46), residues: 134 sheet: 1.06 (0.29), residues: 288 loop : -0.12 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.032 0.002 TYR C 43 PHE 0.012 0.001 PHE A 19 TRP 0.007 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7198) covalent geometry : angle 0.57049 / 0.30 ( 9756) SS BOND : bond 0.00180 / 0.12 ( 9) SS BOND : angle 0.42568 / 0.27 ( 18) hydrogen bonds : bond 0.03423 / 2.16 ( 246) hydrogen bonds : angle 5.89039 / 4.06 ( 624) link_ALPHA1-2 : bond 0.00083 / 0.04 ( 1) link_ALPHA1-2 : angle 1.78960 / 1.16 ( 3) link_ALPHA1-3 : bond 0.00640 / 0.34 ( 1) link_ALPHA1-3 : angle 1.31716 / 0.84 ( 3) link_ALPHA1-6 : bond 0.00499 / 0.26 ( 1) link_ALPHA1-6 : angle 1.30372 / 1.17 ( 3) link_BETA1-4 : bond 0.01181 / 0.57 ( 5) link_BETA1-4 : angle 2.47739 / 1.50 ( 15) link_NAG-ASN : bond 0.00999 / 0.48 ( 8) link_NAG-ASN : angle 2.96220 / 2.20 ( 24) *********************** 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 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.270 Fit side-chains REVERT: A 117 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: A 275 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: A 369 LYS cc_start: 0.7827 (mmpt) cc_final: 0.7148 (mtpt) REVERT: B 112 ASP cc_start: 0.8089 (t0) cc_final: 0.7855 (t0) REVERT: B 133 ARG cc_start: 0.8112 (ptp-110) cc_final: 0.7214 (ppp-140) REVERT: B 204 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 271 VAL cc_start: 0.8435 (p) cc_final: 0.8154 (t) REVERT: B 394 MET cc_start: 0.6357 (tpt) cc_final: 0.5928 (tpt) REVERT: C 6 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7465 (ttt180) REVERT: C 46 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.8004 (t) REVERT: C 71 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7192 (mp0) outliers start: 17 outliers final: 8 residues processed: 86 average time/residue: 0.4435 time to fit residues: 40.6019 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 : 0.271 ------------------------------------------------------------------------------- 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 275 TYR 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 46 VAL Chi-restraints excluded: chain C residue 70 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 54 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107398 restraints weight = 10060.504| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.54 r_work: 0.3268 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 7223 Z= 0.276 Angle : 0.726 9.226 9822 Z= 0.367 Chirality : 0.052 0.203 1107 Planarity : 0.005 0.046 1260 Dihedral : 4.946 18.221 945 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.48 % Favored : 95.40 % Rotamer: Outliers : 2.84 % Allowed : 15.43 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.28), residues: 870 helix: -0.65 (0.44), residues: 134 sheet: 0.87 (0.30), residues: 279 loop : -0.40 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 437 TYR 0.034 0.003 TYR C 43 PHE 0.022 0.002 PHE A 163 TRP 0.010 0.002 TRP A 179 HIS 0.007 0.002 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 ( 7198) covalent geometry : angle 0.70074 / 0.36 ( 9756) SS BOND : bond 0.00313 / 0.21 ( 9) SS BOND : angle 0.71189 / 0.46 ( 18) hydrogen bonds : bond 0.04403 / 2.74 ( 246) hydrogen bonds : angle 6.27594 / 4.37 ( 624) link_ALPHA1-2 : bond 0.00232 / 0.12 ( 1) link_ALPHA1-2 : angle 1.94257 / 1.20 ( 3) link_ALPHA1-3 : bond 0.00823 / 0.43 ( 1) link_ALPHA1-3 : angle 1.53048 / 0.89 ( 3) link_ALPHA1-6 : bond 0.00240 / 0.13 ( 1) link_ALPHA1-6 : angle 1.53451 / 1.45 ( 3) link_BETA1-4 : bond 0.01260 / 0.61 ( 5) link_BETA1-4 : angle 2.79184 / 1.69 ( 15) link_NAG-ASN : bond 0.00976 / 0.47 ( 8) link_NAG-ASN : angle 3.12634 / 2.35 ( 24) *********************** 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 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.198 Fit side-chains REVERT: A 101 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7753 (tptm) REVERT: A 117 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8226 (mm-30) REVERT: A 369 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7426 (mtmt) REVERT: A 372 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7802 (mm) REVERT: B 133 ARG cc_start: 0.8093 (ptp-110) cc_final: 0.7241 (ppp-140) REVERT: B 204 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 271 VAL cc_start: 0.8551 (p) cc_final: 0.8284 (t) REVERT: B 394 MET cc_start: 0.6558 (tpt) cc_final: 0.6195 (tpt) REVERT: C 6 ARG cc_start: 0.8108 (ttt90) cc_final: 0.7631 (ttt180) REVERT: C 55 LYS cc_start: 0.7312 (mtmm) cc_final: 0.6694 (mptt) REVERT: C 71 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7457 (mp0) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 0.5203 time to fit residues: 51.1825 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 A residue 372 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 62 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110849 restraints weight = 10024.562| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.54 r_work: 0.3316 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7223 Z= 0.151 Angle : 0.639 11.742 9822 Z= 0.321 Chirality : 0.048 0.168 1107 Planarity : 0.004 0.039 1260 Dihedral : 4.682 17.508 945 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.24 % Rotamer: Outliers : 1.89 % Allowed : 16.37 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 870 helix: -0.30 (0.46), residues: 133 sheet: 0.87 (0.30), residues: 279 loop : -0.34 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.035 0.002 TYR C 43 PHE 0.025 0.001 PHE B 93 TRP 0.007 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7198) covalent geometry : angle 0.61447 / 0.32 ( 9756) SS BOND : bond 0.00170 / 0.11 ( 9) SS BOND : angle 0.48636 / 0.30 ( 18) hydrogen bonds : bond 0.03564 / 2.24 ( 246) hydrogen bonds : angle 6.12454 / 4.26 ( 624) link_ALPHA1-2 : bond 0.00137 / 0.07 ( 1) link_ALPHA1-2 : angle 1.76741 / 1.13 ( 3) link_ALPHA1-3 : bond 0.00645 / 0.34 ( 1) link_ALPHA1-3 : angle 1.33707 / 0.83 ( 3) link_ALPHA1-6 : bond 0.00504 / 0.27 ( 1) link_ALPHA1-6 : angle 1.27485 / 1.15 ( 3) link_BETA1-4 : bond 0.01209 / 0.60 ( 5) link_BETA1-4 : angle 2.61843 / 1.57 ( 15) link_NAG-ASN : bond 0.01272 / 0.62 ( 8) link_NAG-ASN : angle 2.87566 / 2.23 ( 24) *********************** 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 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.161 Fit side-chains REVERT: A 117 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: A 148 ASP cc_start: 0.8028 (m-30) cc_final: 0.7354 (t0) REVERT: A 203 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8020 (tmmt) REVERT: A 369 LYS cc_start: 0.7867 (mmpt) cc_final: 0.7295 (mtpt) REVERT: B 133 ARG cc_start: 0.8148 (ptp-110) cc_final: 0.7240 (ppp-140) REVERT: B 204 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7918 (tt) REVERT: B 271 VAL cc_start: 0.8547 (p) cc_final: 0.8274 (t) REVERT: B 370 ARG cc_start: 0.8095 (mmt180) cc_final: 0.7682 (mmt90) REVERT: B 394 MET cc_start: 0.6240 (tpt) cc_final: 0.5814 (tpt) REVERT: C 6 ARG cc_start: 0.8058 (ttt90) cc_final: 0.7594 (ttt180) REVERT: C 55 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6851 (mptt) REVERT: C 71 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7374 (mp0) outliers start: 14 outliers final: 8 residues processed: 87 average time/residue: 0.4001 time to fit residues: 37.1343 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 A residue 308 LYS 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 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.138191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111186 restraints weight = 9974.336| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.55 r_work: 0.3322 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4458 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= 0.146 Angle : 0.641 16.487 9822 Z= 0.321 Chirality : 0.048 0.252 1107 Planarity : 0.004 0.035 1260 Dihedral : 4.615 17.771 945 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 1.89 % Allowed : 16.37 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 870 helix: -0.25 (0.46), residues: 133 sheet: 0.83 (0.30), residues: 279 loop : -0.33 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 248 TYR 0.016 0.002 TYR A 178 PHE 0.024 0.001 PHE B 93 TRP 0.007 0.001 TRP A 179 HIS 0.008 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7198) covalent geometry : angle 0.61968 / 0.32 ( 9756) SS BOND : bond 0.00171 / 0.12 ( 9) SS BOND : angle 0.41511 / 0.26 ( 18) hydrogen bonds : bond 0.03511 / 2.22 ( 246) hydrogen bonds : angle 6.07498 / 4.23 ( 624) link_ALPHA1-2 : bond 0.00185 / 0.10 ( 1) link_ALPHA1-2 : angle 1.70201 / 1.12 ( 3) link_ALPHA1-3 : bond 0.00695 / 0.37 ( 1) link_ALPHA1-3 : angle 1.36736 / 0.87 ( 3) link_ALPHA1-6 : bond 0.00403 / 0.21 ( 1) link_ALPHA1-6 : angle 1.26331 / 1.14 ( 3) link_BETA1-4 : bond 0.01180 / 0.57 ( 5) link_BETA1-4 : angle 2.51032 / 1.51 ( 15) link_NAG-ASN : bond 0.01312 / 0.65 ( 8) link_NAG-ASN : angle 2.68662 / 2.03 ( 24) ********************** 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.258 Fit side-chains REVERT: A 117 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: A 132 ASP cc_start: 0.7626 (p0) cc_final: 0.7375 (p0) REVERT: A 148 ASP cc_start: 0.8073 (m-30) cc_final: 0.7432 (t0) REVERT: A 203 LYS cc_start: 0.8274 (ttpp) cc_final: 0.8016 (tmmt) REVERT: A 275 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: A 369 LYS cc_start: 0.7835 (mmpt) cc_final: 0.7333 (mtmt) REVERT: B 133 ARG cc_start: 0.8172 (ptp-110) cc_final: 0.7267 (ppp-140) REVERT: B 204 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7893 (tt) REVERT: B 271 VAL cc_start: 0.8545 (p) cc_final: 0.8277 (t) REVERT: B 370 ARG cc_start: 0.8153 (mmt180) cc_final: 0.7781 (mmt90) REVERT: B 394 MET cc_start: 0.6227 (tpt) cc_final: 0.5747 (tpt) REVERT: C 6 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7521 (ttt180) REVERT: C 43 TYR cc_start: 0.8460 (p90) cc_final: 0.8126 (p90) REVERT: C 55 LYS cc_start: 0.7225 (mtmm) cc_final: 0.6855 (mptt) REVERT: C 71 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7405 (mp0) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.4164 time to fit residues: 39.9219 Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 A residue 275 TYR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain B residue 112 ASP 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 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.138855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111859 restraints weight = 9900.228| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.53 r_work: 0.3335 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7223 Z= 0.135 Angle : 0.643 18.217 9822 Z= 0.320 Chirality : 0.050 0.529 1107 Planarity : 0.004 0.037 1260 Dihedral : 4.563 17.743 945 Min Nonbonded Distance : 1.938 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 870 helix: -0.15 (0.46), residues: 133 sheet: 0.86 (0.30), residues: 279 loop : -0.33 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 248 TYR 0.016 0.002 TYR A 178 PHE 0.012 0.001 PHE A 19 TRP 0.008 0.001 TRP A 179 HIS 0.007 0.001 HIS C 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7198) covalent geometry : angle 0.61577 / 0.31 ( 9756) SS BOND : bond 0.00168 / 0.12 ( 9) SS BOND : angle 0.39426 / 0.24 ( 18) hydrogen bonds : bond 0.03425 / 2.17 ( 246) hydrogen bonds : angle 6.06383 / 4.24 ( 624) link_ALPHA1-2 : bond 0.00189 / 0.10 ( 1) link_ALPHA1-2 : angle 1.68245 / 1.13 ( 3) link_ALPHA1-3 : bond 0.00621 / 0.33 ( 1) link_ALPHA1-3 : angle 1.33154 / 0.86 ( 3) link_ALPHA1-6 : bond 0.00507 / 0.27 ( 1) link_ALPHA1-6 : angle 1.29500 / 1.16 ( 3) link_BETA1-4 : bond 0.01169 / 0.57 ( 5) link_BETA1-4 : angle 2.45898 / 1.48 ( 15) link_NAG-ASN : bond 0.01256 / 0.61 ( 8) link_NAG-ASN : angle 3.21755 / 2.67 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.82 seconds wall clock time: 36 minutes 6.85 seconds (2166.85 seconds total)