Starting phenix.real_space_refine on Tue Mar 3 20:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uja_20794/03_2026/6uja_20794.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uja_20794/03_2026/6uja_20794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uja_20794/03_2026/6uja_20794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uja_20794/03_2026/6uja_20794.map" model { file = "/net/cci-nas-00/data/ceres_data/6uja_20794/03_2026/6uja_20794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uja_20794/03_2026/6uja_20794.cif" } resolution = 3.3 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= 0.003 sd= 0.077 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 32 5.16 5 C 5149 2.51 5 N 1419 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8224 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4242 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASN:plan1': 7, 'GLU:plan': 7, 'TYR:plan': 4, 'GLN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 6, 'ARG:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 200 Chain: "B" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 939 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 2 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLU:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 7, 'ARG:plan': 14, 'ASP:plan': 5, 'GLN:plan1': 4, 'PHE:plan': 5, 'HIS:plan': 4, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 297 Chain: "C" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.98, per 1000 atoms: 0.24 Number of scatterers: 8224 At special positions: 0 Unit cell: (72.63, 100.875, 151.985, 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 32 16.00 Mg 1 11.99 O 1618 8.00 N 1419 7.00 C 5149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.05 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.02 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 C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A2005 " - " ASN A 260 " " NAG B2005 " - " ASN B 360 " " NAG B2010 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG E 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 191 " " NAG G 1 " - " ASN B 389 " " NAG H 1 " - " ASN B 414 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 324.7 milliseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 15.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 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 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.971A 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 'D' and resid 45 through 55 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.985A pdb=" N PHE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 removed outlier: 3.582A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 215 through 224 removed outlier: 4.301A pdb=" N LEU D 218 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR D 220 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS D 222 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.277A pdb=" N THR A 412 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 423 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY A 410 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY A 425 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET A 408 " --> pdb=" O GLY A 425 " (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: 7.049A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.680A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.560A 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: 6.558A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.648A 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: 6.390A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.217A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N SER A 471 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.217A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.581A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.296A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 78 through 83 Processing sheet with id=AB9, first strand: chain 'D' and resid 101 through 107 removed outlier: 6.450A pdb=" N GLY D 187 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 144 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLN D 143 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR D 152 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR D 145 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP D 150 " --> pdb=" O TYR D 145 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 1.01 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: 1905 1.32 - 1.45: 2186 1.45 - 1.58: 4232 1.58 - 1.71: 5 1.71 - 1.84: 50 Bond restraints: 8378 Sorted by residual: bond pdb=" CB HIS B 184 " pdb=" CG HIS B 184 " ideal model delta sigma weight residual 1.497 1.449 0.048 1.40e-02 5.10e+03 1.18e+01 bond pdb=" C5 NAG B2010 " pdb=" O5 NAG B2010 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.453 -0.069 2.10e-02 2.27e+03 1.06e+01 ... (remaining 8373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.10: 11414 8.10 - 16.20: 4 16.20 - 24.30: 0 24.30 - 32.41: 0 32.41 - 40.51: 1 Bond angle restraints: 11419 Sorted by residual: angle pdb=" C2 NAG G 2 " pdb=" N2 NAG G 2 " pdb=" C7 NAG G 2 " ideal model delta sigma weight residual 124.56 165.07 -40.51 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 127.75 -8.19 1.02e+00 9.61e-01 6.44e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.28 128.09 -8.81 1.10e+00 8.26e-01 6.42e+01 angle pdb=" C GLY A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta sigma weight residual 119.56 127.63 -8.07 1.01e+00 9.80e-01 6.38e+01 angle pdb=" C GLU D 117 " pdb=" N PRO D 118 " pdb=" CA PRO D 118 " ideal model delta sigma weight residual 119.87 128.01 -8.14 1.04e+00 9.25e-01 6.13e+01 ... (remaining 11414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 5075 21.38 - 42.75: 101 42.75 - 64.13: 26 64.13 - 85.50: 15 85.50 - 106.88: 6 Dihedral angle restraints: 5223 sinusoidal: 1985 harmonic: 3238 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 37.73 55.27 1 1.00e+01 1.00e-02 4.13e+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 -118.26 32.26 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.17 106.88 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 941 0.072 - 0.143: 295 0.143 - 0.215: 59 0.215 - 0.287: 29 0.287 - 0.359: 18 Chirality restraints: 1342 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.14e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.27 0.13 2.00e-02 2.50e+03 4.26e+01 chirality pdb=" C1 MAN C 5 " pdb=" O2 MAN C 4 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 1.03e+01 ... (remaining 1339 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.08e-02 1.19e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.029 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" CG ASN A 44 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.048 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 172 " 0.043 2.00e-02 2.50e+03 2.24e-02 1.01e+01 pdb=" CG TYR B 172 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 172 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 172 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 172 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 172 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 172 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 172 " 0.032 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 29 2.42 - 3.04: 5151 3.04 - 3.66: 11604 3.66 - 4.28: 18614 4.28 - 4.90: 30127 Nonbonded interactions: 65525 Sorted by model distance: nonbonded pdb=" OD1 ASP D 217 " pdb="MG MG B2002 " model vdw 1.802 2.170 nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.813 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 1.973 2.170 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.088 2.510 nonbonded pdb=" OD1 ASP A 413 " pdb="CA CA A2003 " model vdw 2.096 2.510 ... (remaining 65520 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' selection = chain 'H' } 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: 1.810 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.095 8402 Z= 0.788 Angle : 1.501 40.507 11484 Z= 0.987 Chirality : 0.086 0.359 1342 Planarity : 0.006 0.033 1508 Dihedral : 11.587 106.875 3120 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.69 % Favored : 97.13 % Rotamer: Outliers : 0.14 % Allowed : 0.69 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.28 (0.24), residues: 1116 helix: -1.31 (0.37), residues: 132 sheet: 1.12 (0.24), residues: 384 loop : -0.01 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 231 TYR 0.043 0.006 TYR B 172 PHE 0.026 0.004 PHE A 276 TRP 0.023 0.007 TRP B 230 HIS 0.006 0.002 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.01418 ( 8378) covalent geometry : angle 1.48697 (11419) SS BOND : bond 0.00951 ( 7) SS BOND : angle 3.05362 ( 14) hydrogen bonds : bond 0.16595 ( 317) hydrogen bonds : angle 8.90277 ( 813) link_ALPHA1-2 : bond 0.07266 ( 1) link_ALPHA1-2 : angle 3.99078 ( 3) link_ALPHA1-3 : bond 0.07331 ( 1) link_ALPHA1-3 : angle 3.58036 ( 3) link_ALPHA1-6 : bond 0.05437 ( 1) link_ALPHA1-6 : angle 2.98845 ( 3) link_BETA1-4 : bond 0.06249 ( 6) link_BETA1-4 : angle 3.55638 ( 18) link_NAG-ASN : bond 0.06881 ( 8) link_NAG-ASN : angle 2.55928 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7565 (t0) cc_final: 0.7257 (t0) REVERT: A 310 GLN cc_start: 0.7968 (mt0) cc_final: 0.7764 (mt0) REVERT: B 135 MET cc_start: 0.8261 (mmm) cc_final: 0.7916 (mmt) REVERT: B 173 ASN cc_start: 0.8626 (t0) cc_final: 0.8402 (t0) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1184 time to fit residues: 20.1038 Evaluate side-chains 61 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098985 restraints weight = 13224.220| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.33 r_work: 0.3108 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8402 Z= 0.200 Angle : 0.676 9.933 11484 Z= 0.352 Chirality : 0.049 0.205 1342 Planarity : 0.004 0.032 1508 Dihedral : 7.959 84.931 1541 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 1.52 % Allowed : 6.65 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.32 (0.25), residues: 1116 helix: -0.14 (0.45), residues: 126 sheet: 0.68 (0.24), residues: 415 loop : 0.05 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 226 TYR 0.018 0.002 TYR A 112 PHE 0.014 0.002 PHE A 276 TRP 0.011 0.002 TRP A 179 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 8378) covalent geometry : angle 0.64284 (11419) SS BOND : bond 0.00718 ( 7) SS BOND : angle 2.12879 ( 14) hydrogen bonds : bond 0.04151 ( 317) hydrogen bonds : angle 6.64697 ( 813) link_ALPHA1-2 : bond 0.00782 ( 1) link_ALPHA1-2 : angle 1.70769 ( 3) link_ALPHA1-3 : bond 0.01413 ( 1) link_ALPHA1-3 : angle 1.14251 ( 3) link_ALPHA1-6 : bond 0.01095 ( 1) link_ALPHA1-6 : angle 1.56089 ( 3) link_BETA1-4 : bond 0.01246 ( 6) link_BETA1-4 : angle 3.31322 ( 18) link_NAG-ASN : bond 0.01074 ( 8) link_NAG-ASN : angle 3.25840 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.9022 (t0) cc_final: 0.8275 (t0) REVERT: A 165 LYS cc_start: 0.8406 (pttt) cc_final: 0.8180 (pttt) REVERT: A 310 GLN cc_start: 0.8515 (mt0) cc_final: 0.8285 (mt0) REVERT: B 103 TYR cc_start: 0.8827 (m-80) cc_final: 0.8552 (m-80) REVERT: B 135 MET cc_start: 0.8903 (mmm) cc_final: 0.8520 (mmt) REVERT: B 173 ASN cc_start: 0.9042 (t0) cc_final: 0.8841 (t0) outliers start: 11 outliers final: 5 residues processed: 82 average time/residue: 0.0901 time to fit residues: 10.3013 Evaluate side-chains 67 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.131504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096519 restraints weight = 13242.739| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.37 r_work: 0.3066 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8402 Z= 0.182 Angle : 0.611 9.779 11484 Z= 0.315 Chirality : 0.047 0.239 1342 Planarity : 0.004 0.032 1508 Dihedral : 7.090 73.621 1541 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.08 % Allowed : 6.37 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.26 (0.25), residues: 1116 helix: 0.14 (0.48), residues: 127 sheet: 0.61 (0.24), residues: 421 loop : -0.06 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 226 TYR 0.016 0.002 TYR A 112 PHE 0.015 0.002 PHE A 276 TRP 0.011 0.002 TRP A 179 HIS 0.006 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8378) covalent geometry : angle 0.57815 (11419) SS BOND : bond 0.00199 ( 7) SS BOND : angle 1.59094 ( 14) hydrogen bonds : bond 0.03643 ( 317) hydrogen bonds : angle 6.12433 ( 813) link_ALPHA1-2 : bond 0.00572 ( 1) link_ALPHA1-2 : angle 1.48748 ( 3) link_ALPHA1-3 : bond 0.01377 ( 1) link_ALPHA1-3 : angle 1.50649 ( 3) link_ALPHA1-6 : bond 0.00897 ( 1) link_ALPHA1-6 : angle 1.11128 ( 3) link_BETA1-4 : bond 0.01211 ( 6) link_BETA1-4 : angle 3.01232 ( 18) link_NAG-ASN : bond 0.00916 ( 8) link_NAG-ASN : angle 3.21484 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8352 (t0) cc_final: 0.7988 (t0) REVERT: B 103 TYR cc_start: 0.8850 (m-80) cc_final: 0.8625 (m-80) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.0868 time to fit residues: 8.9996 Evaluate side-chains 65 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096343 restraints weight = 13453.864| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.34 r_work: 0.3067 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8402 Z= 0.152 Angle : 0.569 10.413 11484 Z= 0.290 Chirality : 0.047 0.256 1342 Planarity : 0.004 0.033 1508 Dihedral : 6.587 64.888 1541 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.08 % Allowed : 7.20 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.20 (0.25), residues: 1116 helix: 0.19 (0.49), residues: 128 sheet: 0.63 (0.24), residues: 420 loop : -0.17 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 226 TYR 0.015 0.001 TYR A 112 PHE 0.012 0.001 PHE A 276 TRP 0.010 0.001 TRP A 179 HIS 0.007 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8378) covalent geometry : angle 0.53845 (11419) SS BOND : bond 0.00209 ( 7) SS BOND : angle 0.97240 ( 14) hydrogen bonds : bond 0.03144 ( 317) hydrogen bonds : angle 5.78357 ( 813) link_ALPHA1-2 : bond 0.00402 ( 1) link_ALPHA1-2 : angle 1.42856 ( 3) link_ALPHA1-3 : bond 0.01206 ( 1) link_ALPHA1-3 : angle 1.73751 ( 3) link_ALPHA1-6 : bond 0.00970 ( 1) link_ALPHA1-6 : angle 1.13976 ( 3) link_BETA1-4 : bond 0.01135 ( 6) link_BETA1-4 : angle 2.83161 ( 18) link_NAG-ASN : bond 0.00978 ( 8) link_NAG-ASN : angle 3.13669 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8414 (t0) cc_final: 0.8101 (t0) REVERT: B 103 TYR cc_start: 0.8851 (m-80) cc_final: 0.8606 (m-80) outliers start: 15 outliers final: 8 residues processed: 69 average time/residue: 0.0900 time to fit residues: 8.7452 Evaluate side-chains 64 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095824 restraints weight = 13387.239| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.39 r_work: 0.3057 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8402 Z= 0.153 Angle : 0.562 9.357 11484 Z= 0.286 Chirality : 0.046 0.260 1342 Planarity : 0.004 0.035 1508 Dihedral : 6.337 59.792 1541 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.94 % Allowed : 8.17 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.26 (0.25), residues: 1116 helix: 0.21 (0.49), residues: 129 sheet: 0.79 (0.24), residues: 415 loop : -0.23 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 303 TYR 0.014 0.001 TYR A 112 PHE 0.012 0.001 PHE A 276 TRP 0.007 0.001 TRP A 179 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8378) covalent geometry : angle 0.53360 (11419) SS BOND : bond 0.00246 ( 7) SS BOND : angle 0.93745 ( 14) hydrogen bonds : bond 0.03100 ( 317) hydrogen bonds : angle 5.63636 ( 813) link_ALPHA1-2 : bond 0.00512 ( 1) link_ALPHA1-2 : angle 1.38614 ( 3) link_ALPHA1-3 : bond 0.01242 ( 1) link_ALPHA1-3 : angle 1.83838 ( 3) link_ALPHA1-6 : bond 0.00973 ( 1) link_ALPHA1-6 : angle 1.13805 ( 3) link_BETA1-4 : bond 0.01132 ( 6) link_BETA1-4 : angle 2.76145 ( 18) link_NAG-ASN : bond 0.00867 ( 8) link_NAG-ASN : angle 2.96642 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8364 (t0) cc_final: 0.8108 (t0) REVERT: A 146 ASP cc_start: 0.8955 (t0) cc_final: 0.8677 (t0) REVERT: A 379 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7667 (mtt-85) REVERT: B 103 TYR cc_start: 0.8925 (m-80) cc_final: 0.8636 (m-80) REVERT: B 218 MET cc_start: 0.9210 (mtp) cc_final: 0.9007 (mtm) REVERT: B 355 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8151 (tp-100) REVERT: B 371 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7044 (mmmt) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 0.1023 time to fit residues: 9.8501 Evaluate side-chains 70 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 0.0570 chunk 85 optimal weight: 0.0040 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096636 restraints weight = 13210.635| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.31 r_work: 0.3071 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8402 Z= 0.126 Angle : 0.532 9.132 11484 Z= 0.270 Chirality : 0.046 0.260 1342 Planarity : 0.003 0.028 1508 Dihedral : 6.104 55.794 1541 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.80 % Allowed : 8.45 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.29 (0.25), residues: 1116 helix: 0.28 (0.49), residues: 129 sheet: 0.81 (0.24), residues: 417 loop : -0.23 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.012 0.001 TYR A 112 PHE 0.011 0.001 PHE A 276 TRP 0.006 0.001 TRP A 179 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8378) covalent geometry : angle 0.50356 (11419) SS BOND : bond 0.00208 ( 7) SS BOND : angle 0.75206 ( 14) hydrogen bonds : bond 0.02865 ( 317) hydrogen bonds : angle 5.49553 ( 813) link_ALPHA1-2 : bond 0.00492 ( 1) link_ALPHA1-2 : angle 1.38842 ( 3) link_ALPHA1-3 : bond 0.01358 ( 1) link_ALPHA1-3 : angle 1.99964 ( 3) link_ALPHA1-6 : bond 0.00989 ( 1) link_ALPHA1-6 : angle 1.12874 ( 3) link_BETA1-4 : bond 0.01126 ( 6) link_BETA1-4 : angle 2.65518 ( 18) link_NAG-ASN : bond 0.01121 ( 8) link_NAG-ASN : angle 2.89181 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7866 (ptt) REVERT: A 146 ASP cc_start: 0.8970 (t0) cc_final: 0.8653 (t0) REVERT: A 379 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7721 (mtt-85) REVERT: B 103 TYR cc_start: 0.8964 (m-80) cc_final: 0.8559 (m-80) REVERT: B 236 ARG cc_start: 0.8715 (mtt180) cc_final: 0.8513 (mtt180) REVERT: B 355 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8172 (tp-100) REVERT: B 371 LYS cc_start: 0.7422 (mmtt) cc_final: 0.7048 (mmmt) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.1035 time to fit residues: 10.6482 Evaluate side-chains 76 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 50.0000 chunk 46 optimal weight: 30.0000 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093431 restraints weight = 13512.847| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.31 r_work: 0.3020 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8402 Z= 0.232 Angle : 0.622 10.068 11484 Z= 0.316 Chirality : 0.049 0.250 1342 Planarity : 0.004 0.044 1508 Dihedral : 6.369 53.402 1541 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.22 % Allowed : 9.14 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.10 (0.24), residues: 1116 helix: 0.10 (0.48), residues: 126 sheet: 0.74 (0.24), residues: 412 loop : -0.39 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 245 TYR 0.019 0.002 TYR A 112 PHE 0.018 0.002 PHE A 326 TRP 0.010 0.002 TRP A 179 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 8378) covalent geometry : angle 0.59553 (11419) SS BOND : bond 0.00353 ( 7) SS BOND : angle 1.10134 ( 14) hydrogen bonds : bond 0.03373 ( 317) hydrogen bonds : angle 5.74975 ( 813) link_ALPHA1-2 : bond 0.00502 ( 1) link_ALPHA1-2 : angle 1.29320 ( 3) link_ALPHA1-3 : bond 0.01403 ( 1) link_ALPHA1-3 : angle 2.01593 ( 3) link_ALPHA1-6 : bond 0.00674 ( 1) link_ALPHA1-6 : angle 1.31861 ( 3) link_BETA1-4 : bond 0.01078 ( 6) link_BETA1-4 : angle 2.92168 ( 18) link_NAG-ASN : bond 0.01166 ( 8) link_NAG-ASN : angle 2.92163 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7900 (ptt) REVERT: A 275 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8598 (t80) REVERT: B 103 TYR cc_start: 0.9135 (m-80) cc_final: 0.8639 (m-80) REVERT: B 355 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8181 (tp-100) REVERT: B 371 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7129 (mmmt) outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 0.0864 time to fit residues: 9.4239 Evaluate side-chains 73 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 34 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095737 restraints weight = 13347.972| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.30 r_work: 0.3061 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8402 Z= 0.130 Angle : 0.541 9.266 11484 Z= 0.275 Chirality : 0.046 0.247 1342 Planarity : 0.003 0.031 1508 Dihedral : 6.028 51.349 1541 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.66 % Allowed : 9.97 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.28 (0.25), residues: 1116 helix: 0.63 (0.51), residues: 120 sheet: 0.82 (0.25), residues: 414 loop : -0.33 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 226 TYR 0.012 0.001 TYR A 112 PHE 0.011 0.001 PHE A 276 TRP 0.008 0.001 TRP B 230 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8378) covalent geometry : angle 0.51459 (11419) SS BOND : bond 0.00203 ( 7) SS BOND : angle 0.69317 ( 14) hydrogen bonds : bond 0.02831 ( 317) hydrogen bonds : angle 5.45426 ( 813) link_ALPHA1-2 : bond 0.00498 ( 1) link_ALPHA1-2 : angle 1.37074 ( 3) link_ALPHA1-3 : bond 0.01371 ( 1) link_ALPHA1-3 : angle 2.00714 ( 3) link_ALPHA1-6 : bond 0.00980 ( 1) link_ALPHA1-6 : angle 1.08973 ( 3) link_BETA1-4 : bond 0.01107 ( 6) link_BETA1-4 : angle 2.66673 ( 18) link_NAG-ASN : bond 0.01317 ( 8) link_NAG-ASN : angle 2.70808 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7961 (ptt) REVERT: A 379 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7612 (mtt-85) REVERT: B 103 TYR cc_start: 0.9024 (m-80) cc_final: 0.8590 (m-80) REVERT: B 320 ILE cc_start: 0.8852 (tp) cc_final: 0.8465 (pt) REVERT: B 355 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8195 (tp-100) REVERT: B 371 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7100 (mmmt) outliers start: 12 outliers final: 6 residues processed: 75 average time/residue: 0.1189 time to fit residues: 11.8426 Evaluate side-chains 72 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093956 restraints weight = 13395.859| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.35 r_work: 0.3028 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8402 Z= 0.204 Angle : 0.597 9.789 11484 Z= 0.302 Chirality : 0.048 0.243 1342 Planarity : 0.004 0.036 1508 Dihedral : 6.157 55.079 1541 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.08 % Allowed : 10.11 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.17 (0.25), residues: 1116 helix: 0.49 (0.51), residues: 120 sheet: 0.77 (0.25), residues: 412 loop : -0.40 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 303 TYR 0.016 0.002 TYR A 112 PHE 0.015 0.002 PHE A 276 TRP 0.009 0.002 TRP A 179 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8378) covalent geometry : angle 0.57264 (11419) SS BOND : bond 0.00264 ( 7) SS BOND : angle 0.93148 ( 14) hydrogen bonds : bond 0.03118 ( 317) hydrogen bonds : angle 5.56428 ( 813) link_ALPHA1-2 : bond 0.00546 ( 1) link_ALPHA1-2 : angle 1.30055 ( 3) link_ALPHA1-3 : bond 0.01484 ( 1) link_ALPHA1-3 : angle 2.11364 ( 3) link_ALPHA1-6 : bond 0.00729 ( 1) link_ALPHA1-6 : angle 1.23372 ( 3) link_BETA1-4 : bond 0.01036 ( 6) link_BETA1-4 : angle 2.84225 ( 18) link_NAG-ASN : bond 0.01362 ( 8) link_NAG-ASN : angle 2.67174 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8020 (ptt) REVERT: A 275 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8533 (t80) REVERT: B 103 TYR cc_start: 0.9108 (m-80) cc_final: 0.8520 (m-80) REVERT: B 268 LYS cc_start: 0.7076 (ttmm) cc_final: 0.6695 (mttp) REVERT: B 355 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8213 (tp-100) REVERT: B 371 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7084 (mmmt) REVERT: D 214 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8182 (tpp-160) outliers start: 15 outliers final: 8 residues processed: 75 average time/residue: 0.1261 time to fit residues: 12.3085 Evaluate side-chains 72 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094560 restraints weight = 13301.786| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.36 r_work: 0.3039 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.004 0.041 8402 Z= 0.158 Angle : 0.572 9.375 11484 Z= 0.290 Chirality : 0.047 0.240 1342 Planarity : 0.004 0.035 1508 Dihedral : 6.032 54.532 1541 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.39 % Allowed : 10.94 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.17 (0.25), residues: 1116 helix: 0.55 (0.51), residues: 120 sheet: 0.77 (0.25), residues: 408 loop : -0.41 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 303 TYR 0.013 0.001 TYR A 112 PHE 0.012 0.001 PHE A 276 TRP 0.007 0.001 TRP A 179 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8378) covalent geometry : angle 0.54827 (11419) SS BOND : bond 0.00244 ( 7) SS BOND : angle 0.78944 ( 14) hydrogen bonds : bond 0.02912 ( 317) hydrogen bonds : angle 5.46909 ( 813) link_ALPHA1-2 : bond 0.00525 ( 1) link_ALPHA1-2 : angle 1.33187 ( 3) link_ALPHA1-3 : bond 0.01407 ( 1) link_ALPHA1-3 : angle 2.05420 ( 3) link_ALPHA1-6 : bond 0.00858 ( 1) link_ALPHA1-6 : angle 1.16097 ( 3) link_BETA1-4 : bond 0.01079 ( 6) link_BETA1-4 : angle 2.72846 ( 18) link_NAG-ASN : bond 0.01455 ( 8) link_NAG-ASN : angle 2.63036 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8074 (ptt) REVERT: A 275 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8495 (t80) REVERT: A 379 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7755 (mtt-85) REVERT: B 103 TYR cc_start: 0.9061 (m-80) cc_final: 0.8487 (m-80) REVERT: B 268 LYS cc_start: 0.6981 (ttmm) cc_final: 0.6619 (mttp) REVERT: B 320 ILE cc_start: 0.8846 (tp) cc_final: 0.8472 (pt) REVERT: B 355 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8211 (tp-100) REVERT: B 371 LYS cc_start: 0.7494 (mmtt) cc_final: 0.7062 (mmmt) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.1259 time to fit residues: 11.6914 Evaluate side-chains 73 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 45 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092965 restraints weight = 13425.804| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.34 r_work: 0.3006 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8402 Z= 0.238 Angle : 0.627 10.090 11484 Z= 0.317 Chirality : 0.049 0.235 1342 Planarity : 0.004 0.038 1508 Dihedral : 6.272 59.655 1541 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.66 % Allowed : 11.08 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.00 (0.25), residues: 1116 helix: 0.33 (0.50), residues: 120 sheet: 0.62 (0.25), residues: 407 loop : -0.47 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 201 TYR 0.018 0.002 TYR A 112 PHE 0.016 0.002 PHE A 326 TRP 0.010 0.002 TRP A 179 HIS 0.005 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8378) covalent geometry : angle 0.60200 (11419) SS BOND : bond 0.00341 ( 7) SS BOND : angle 0.97319 ( 14) hydrogen bonds : bond 0.03296 ( 317) hydrogen bonds : angle 5.64477 ( 813) link_ALPHA1-2 : bond 0.00588 ( 1) link_ALPHA1-2 : angle 1.27195 ( 3) link_ALPHA1-3 : bond 0.01523 ( 1) link_ALPHA1-3 : angle 2.15598 ( 3) link_ALPHA1-6 : bond 0.00619 ( 1) link_ALPHA1-6 : angle 1.30070 ( 3) link_BETA1-4 : bond 0.01053 ( 6) link_BETA1-4 : angle 2.88998 ( 18) link_NAG-ASN : bond 0.01493 ( 8) link_NAG-ASN : angle 2.80505 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.99 seconds wall clock time: 36 minutes 0.07 seconds (2160.07 seconds total)