Starting phenix.real_space_refine on Sat Dec 28 01:25:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tcf_41153/12_2024/8tcf_41153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tcf_41153/12_2024/8tcf_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_41153/12_2024/8tcf_41153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tcf_41153/12_2024/8tcf_41153.map" model { file = "/net/cci-nas-00/data/ceres_data/8tcf_41153/12_2024/8tcf_41153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tcf_41153/12_2024/8tcf_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-5532/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: 5.30, per 1000 atoms: 0.75 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: 2.13 Conformation dependent library (CDL) restraints added in 984.3 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: 1.06 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: 2.18 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1285 1.32 - 1.45: 1894 1.45 - 1.58: 3952 1.58 - 1.71: 15 1.71 - 1.84: 52 Bond restraints: 7198 Sorted by residual: bond pdb=" CA SER B 382 " pdb=" CB SER B 382 " ideal model delta sigma weight residual 1.527 1.474 0.054 1.49e-02 4.50e+03 1.29e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.456 -0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" CG PHE A 1 " pdb=" CD2 PHE A 1 " ideal model delta sigma weight residual 1.384 1.453 -0.069 2.10e-02 2.27e+03 1.08e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CG ASP B 209 " pdb=" OD2 ASP B 209 " ideal model delta sigma weight residual 1.249 1.188 0.061 1.90e-02 2.77e+03 1.04e+01 ... (remaining 7193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8112 1.70 - 3.41: 1327 3.41 - 5.11: 227 5.11 - 6.81: 73 6.81 - 8.52: 17 Bond angle restraints: 9756 Sorted by residual: angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 128.08 -8.52 1.02e+00 9.61e-01 6.97e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 127.97 -8.41 1.02e+00 9.61e-01 6.80e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.75 -8.19 1.02e+00 9.61e-01 6.45e+01 angle pdb=" C CYS A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 119.66 125.45 -5.79 7.30e-01 1.88e+00 6.28e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.02e+00 9.61e-01 6.02e+01 ... (remaining 9751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 4349 21.32 - 42.63: 104 42.63 - 63.95: 25 63.95 - 85.26: 16 85.26 - 106.58: 8 Dihedral angle restraints: 4502 sinusoidal: 1987 harmonic: 2515 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 33.56 59.44 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CD ARG B 378 " pdb=" NE ARG B 378 " pdb=" CZ ARG B 378 " pdb=" NH1 ARG B 378 " ideal model delta sinusoidal sigma weight residual 0.00 51.10 -51.10 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS B 397 " pdb=" SG CYS B 397 " pdb=" SG CYS B 425 " pdb=" CB CYS B 425 " ideal model delta sinusoidal sigma weight residual -86.00 -124.83 38.83 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 4499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 771 0.078 - 0.157: 256 0.157 - 0.235: 50 0.235 - 0.313: 15 0.313 - 0.392: 15 Chirality restraints: 1107 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.60e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.51e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.87e+01 ... (remaining 1104 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 378 " 0.863 9.50e-02 1.11e+02 3.87e-01 9.09e+01 pdb=" NE ARG B 378 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 378 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 378 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 378 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2005 " 0.079 2.00e-02 2.50e+03 6.51e-02 5.29e+01 pdb=" C7 NAG B2005 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG B2005 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG B2005 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG B2005 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2003 " 0.071 2.00e-02 2.50e+03 5.86e-02 4.29e+01 pdb=" C7 NAG B2003 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B2003 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG B2003 " -0.094 2.00e-02 2.50e+03 pdb=" O7 NAG B2003 " -0.011 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 29 2.42 - 3.04: 4416 3.04 - 3.66: 10012 3.66 - 4.28: 16815 4.28 - 4.90: 27099 Nonbonded interactions: 58371 Sorted by model distance: nonbonded pdb=" OD1 ASP C 12 " pdb="MG MG B2002 " model vdw 1.804 2.170 nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.809 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASP A 416 " pdb="CA CA A 503 " model vdw 2.093 2.510 nonbonded pdb=" OD1 ASP A 414 " pdb="CA CA A 503 " model vdw 2.097 2.510 ... (remaining 58366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.300 Find NCS groups from input model: 0.090 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- 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 0.080 7198 Z= 0.914 Angle : 1.405 8.517 9756 Z= 0.948 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 *********************** 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 : 0.835 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: 1.2792 time to fit residues: 240.9891 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 : 0.708 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 0.028 7198 Z= 0.219 Angle : 0.660 9.443 9756 Z= 0.346 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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.751 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 114 average time/residue: 1.2032 time to fit residues: 145.1761 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 B 424 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7198 Z= 0.251 Angle : 0.613 6.082 9756 Z= 0.320 Chirality : 0.048 0.252 1107 Planarity : 0.004 0.037 1260 Dihedral : 7.677 71.809 1273 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 2.57 % Allowed : 14.21 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 870 helix: -0.26 (0.45), residues: 134 sheet: 0.80 (0.28), residues: 304 loop : 0.11 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.017 0.002 PHE A 276 TYR 0.023 0.002 TYR C 43 ARG 0.005 0.001 ARG A 437 *********************** 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 103 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.924 Fit side-chains REVERT: B 394 MET cc_start: 0.6256 (tpt) cc_final: 0.5713 (tpt) REVERT: B 418 LYS cc_start: 0.7722 (mtpm) cc_final: 0.7424 (mmmt) REVERT: C 19 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7059 (tppt) outliers start: 19 outliers final: 10 residues processed: 97 average time/residue: 1.0618 time to fit residues: 110.3438 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 308 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 19 LYS 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 77 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7198 Z= 0.292 Angle : 0.626 6.545 9756 Z= 0.326 Chirality : 0.050 0.271 1107 Planarity : 0.005 0.039 1260 Dihedral : 7.494 66.060 1273 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 3.65 % Allowed : 14.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 870 helix: -0.43 (0.45), residues: 134 sheet: 0.92 (0.29), residues: 297 loop : -0.06 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.008 0.002 HIS C 37 PHE 0.018 0.002 PHE A 276 TYR 0.028 0.002 TYR C 43 ARG 0.008 0.001 ARG A 437 *********************** 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: 27 poor density : 78 time to evaluate : 0.794 Fit side-chains REVERT: B 394 MET cc_start: 0.6406 (tpt) cc_final: 0.5899 (tpt) REVERT: C 19 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7109 (tppt) REVERT: C 71 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6665 (mt-10) outliers start: 27 outliers final: 12 residues processed: 92 average time/residue: 1.0113 time to fit residues: 99.7396 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 19 LYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0570 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7198 Z= 0.290 Angle : 0.610 6.525 9756 Z= 0.317 Chirality : 0.050 0.266 1107 Planarity : 0.004 0.038 1260 Dihedral : 7.395 63.321 1273 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 3.65 % Allowed : 14.88 % Favored : 81.46 % 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: 0.15 (0.28), residues: 870 helix: -0.43 (0.45), residues: 134 sheet: 0.93 (0.29), residues: 289 loop : -0.22 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.008 0.001 HIS C 37 PHE 0.017 0.002 PHE A 276 TYR 0.028 0.002 TYR C 43 ARG 0.005 0.001 ARG A 437 *********************** 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 102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.703 Fit side-chains REVERT: B 394 MET cc_start: 0.6326 (tpt) cc_final: 0.5841 (tpt) REVERT: C 13 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7525 (mpp) REVERT: C 19 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7142 (tppt) outliers start: 27 outliers final: 12 residues processed: 91 average time/residue: 1.1390 time to fit residues: 110.1450 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 19 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.0060 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7198 Z= 0.272 Angle : 0.612 6.509 9756 Z= 0.318 Chirality : 0.049 0.265 1107 Planarity : 0.004 0.043 1260 Dihedral : 7.239 60.974 1273 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % Rotamer: Outliers : 2.44 % Allowed : 16.64 % Favored : 80.92 % 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: 0.11 (0.28), residues: 870 helix: -0.43 (0.45), residues: 134 sheet: 0.96 (0.30), residues: 280 loop : -0.27 (0.29), residues: 456 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 0.025 0.002 PHE B 93 TYR 0.029 0.002 TYR C 43 ARG 0.004 0.000 ARG A 437 *********************** 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 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.873 Fit side-chains REVERT: A 369 LYS cc_start: 0.7484 (mmpt) cc_final: 0.7278 (mtmt) REVERT: B 394 MET cc_start: 0.6378 (tpt) cc_final: 0.5868 (tpt) REVERT: C 13 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7483 (mpp) REVERT: C 55 LYS cc_start: 0.7118 (mtmm) cc_final: 0.6842 (mptt) outliers start: 18 outliers final: 13 residues processed: 82 average time/residue: 1.0841 time to fit residues: 95.2237 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 350 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.0020 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7198 Z= 0.202 Angle : 0.571 6.201 9756 Z= 0.296 Chirality : 0.048 0.255 1107 Planarity : 0.004 0.038 1260 Dihedral : 6.915 57.583 1273 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.10 % Favored : 96.78 % Rotamer: Outliers : 2.84 % Allowed : 16.24 % Favored : 80.92 % 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: 0.20 (0.28), residues: 870 helix: -0.27 (0.46), residues: 134 sheet: 1.00 (0.30), residues: 280 loop : -0.23 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.023 0.001 PHE B 93 TYR 0.029 0.002 TYR C 43 ARG 0.003 0.000 ARG A 248 *********************** 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.757 Fit side-chains REVERT: A 101 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7349 (tptm) REVERT: B 394 MET cc_start: 0.6325 (tpt) cc_final: 0.5842 (tpt) REVERT: C 13 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7360 (mpp) REVERT: C 19 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6984 (tppt) outliers start: 21 outliers final: 11 residues processed: 87 average time/residue: 1.0556 time to fit residues: 98.0239 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 101 LYS 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 199 VAL 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 19 LYS Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7198 Z= 0.195 Angle : 0.574 8.748 9756 Z= 0.297 Chirality : 0.047 0.252 1107 Planarity : 0.004 0.037 1260 Dihedral : 6.726 55.105 1273 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % Rotamer: Outliers : 1.76 % Allowed : 17.19 % Favored : 81.06 % 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: 0.23 (0.28), residues: 870 helix: -0.18 (0.46), residues: 134 sheet: 1.02 (0.30), residues: 281 loop : -0.23 (0.30), residues: 455 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 0.021 0.001 PHE B 93 TYR 0.030 0.002 TYR C 43 ARG 0.003 0.000 ARG A 248 *********************** 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 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.798 Fit side-chains REVERT: A 101 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7352 (tptm) REVERT: B 86 ARG cc_start: 0.7130 (mtm110) cc_final: 0.6801 (ptp-110) REVERT: B 394 MET cc_start: 0.6307 (tpt) cc_final: 0.5834 (tpt) REVERT: C 13 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7326 (mpp) REVERT: C 19 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6940 (tppt) REVERT: C 55 LYS cc_start: 0.7100 (mtmm) cc_final: 0.6712 (mptt) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 1.0776 time to fit residues: 95.8076 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 226 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 70 VAL 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 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7198 Z= 0.198 Angle : 0.576 10.610 9756 Z= 0.298 Chirality : 0.048 0.251 1107 Planarity : 0.004 0.035 1260 Dihedral : 6.565 52.664 1273 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.76 % Allowed : 16.91 % Favored : 81.33 % 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: 0.13 (0.48), residues: 126 sheet: 0.92 (0.30), residues: 289 loop : -0.16 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 60 HIS 0.007 0.001 HIS C 37 PHE 0.030 0.001 PHE B 93 TYR 0.013 0.001 TYR A 178 ARG 0.004 0.000 ARG C 6 *********************** 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 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.824 Fit side-chains REVERT: A 101 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7361 (tptm) REVERT: B 86 ARG cc_start: 0.7079 (mtm110) cc_final: 0.6825 (ptp-110) REVERT: B 394 MET cc_start: 0.6302 (tpt) cc_final: 0.5838 (tpt) REVERT: C 13 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7380 (mpp) REVERT: C 55 LYS cc_start: 0.7030 (mtmm) cc_final: 0.6815 (mptt) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 1.1019 time to fit residues: 95.4854 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 101 LYS 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 199 VAL 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 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7198 Z= 0.210 Angle : 0.584 8.430 9756 Z= 0.303 Chirality : 0.048 0.250 1107 Planarity : 0.004 0.035 1260 Dihedral : 6.496 51.072 1273 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 1.89 % Allowed : 16.91 % Favored : 81.19 % 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: 0.13 (0.48), residues: 126 sheet: 1.03 (0.30), residues: 280 loop : -0.19 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.006 0.001 HIS C 37 PHE 0.028 0.001 PHE B 93 TYR 0.032 0.002 TYR C 43 ARG 0.005 0.000 ARG A 33 ********************** 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 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.851 Fit side-chains REVERT: A 101 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7367 (tptm) REVERT: B 86 ARG cc_start: 0.7112 (mtm110) cc_final: 0.6903 (ptp-170) REVERT: B 394 MET cc_start: 0.6308 (tpt) cc_final: 0.5847 (tpt) REVERT: C 13 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7376 (mpp) REVERT: C 55 LYS cc_start: 0.7063 (mtmm) cc_final: 0.6835 (mptt) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 1.1112 time to fit residues: 98.4483 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 101 LYS 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 199 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.138935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112167 restraints weight = 9753.283| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.48 r_work: 0.3347 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7198 Z= 0.204 Angle : 0.581 7.735 9756 Z= 0.301 Chirality : 0.048 0.244 1107 Planarity : 0.004 0.035 1260 Dihedral : 6.416 49.571 1273 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 1.89 % Allowed : 17.05 % Favored : 81.06 % 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 (0.29), residues: 870 helix: 0.17 (0.48), residues: 126 sheet: 0.87 (0.30), residues: 289 loop : -0.16 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 179 HIS 0.005 0.001 HIS C 37 PHE 0.025 0.001 PHE B 93 TYR 0.015 0.001 TYR A 178 ARG 0.003 0.000 ARG C 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2754.77 seconds wall clock time: 52 minutes 18.54 seconds (3138.54 seconds total)