Starting phenix.real_space_refine on Fri Sep 11 07:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uja_20794/09_2026/6uja_20794.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uja_20794/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uja_20794/09_2026/6uja_20794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uja_20794/09_2026/6uja_20794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uja_20794/09_2026/6uja_20794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uja_20794/09_2026/6uja_20794.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uja_20794/09_2026/6uja_20794.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uja_20794/09_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-2.2.1-6174/lib/python3.11/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 chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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 chiralities: 2 Time building chain proxies: 1.38, per 1000 atoms: 0.17 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: 0.56 Conformation dependent library (CDL) restraints added in 274.7 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: 0.28 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: 1.35 Time building geometry restraints manager: 0.71 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 - 17.77: 4713 17.77 - 35.54: 113 35.54 - 53.30: 26 53.30 - 71.07: 14 71.07 - 88.84: 8 Dihedral angle restraints: 4874 sinusoidal: 1636 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=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4871 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 10.456 88.842 2771 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/Z covalent geometry : bond 0.01418 / 0.77 ( 8378) covalent geometry : angle 1.48697 / 0.99 (11419) SS BOND : bond 0.00951 / 0.45 ( 7) SS BOND : angle 3.05362 / 1.87 ( 14) hydrogen bonds : bond 0.16595 / 10.77 ( 317) hydrogen bonds : angle 8.90277 / 6.20 ( 813) link_ALPHA1-2 : bond 0.07266 / 3.82 ( 1) link_ALPHA1-2 : angle 3.99078 / 2.72 ( 3) link_ALPHA1-3 : bond 0.07331 / 3.86 ( 1) link_ALPHA1-3 : angle 3.58036 / 2.51 ( 3) link_ALPHA1-6 : bond 0.05437 / 2.86 ( 1) link_ALPHA1-6 : angle 2.98845 / 1.77 ( 3) link_BETA1-4 : bond 0.06249 / 3.37 ( 6) link_BETA1-4 : angle 3.55638 / 2.10 ( 18) link_NAG-ASN : bond 0.06881 / 3.61 ( 8) link_NAG-ASN : angle 2.55928 / 1.82 ( 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 : 0.303 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: 0.1178 time to fit residues: 20.2701 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 : 0.222 ------------------------------------------------------------------------------- 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... ** 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 = 0.133552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098870 restraints weight = 13226.573| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.36 r_work: 0.3106 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8402 Z= 0.198 Angle : 0.678 9.491 11484 Z= 0.352 Chirality : 0.048 0.181 1342 Planarity : 0.004 0.029 1508 Dihedral : 4.901 20.541 1192 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 1.66 % Allowed : 6.51 % 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: 0.69 (0.24), residues: 414 loop : 0.04 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 226 TYR 0.019 0.002 TYR A 112 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.002 TRP A 179 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 8378) covalent geometry : angle 0.64512 / 0.34 (11419) SS BOND : bond 0.00912 / 0.40 ( 7) SS BOND : angle 2.18330 / 0.98 ( 14) hydrogen bonds : bond 0.04115 / 2.56 ( 317) hydrogen bonds : angle 6.66375 / 4.58 ( 813) link_ALPHA1-2 : bond 0.00042 / 0.02 ( 1) link_ALPHA1-2 : angle 1.53779 / 1.14 ( 3) link_ALPHA1-3 : bond 0.01027 / 0.54 ( 1) link_ALPHA1-3 : angle 1.66968 / 0.98 ( 3) link_ALPHA1-6 : bond 0.00054 / 0.03 ( 1) link_ALPHA1-6 : angle 1.74226 / 1.49 ( 3) link_BETA1-4 : bond 0.01198 / 0.58 ( 6) link_BETA1-4 : angle 3.15528 / 1.94 ( 18) link_NAG-ASN : bond 0.01242 / 0.59 ( 8) link_NAG-ASN : angle 3.23118 / 2.31 ( 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 88 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.9025 (t0) cc_final: 0.8272 (t0) REVERT: A 165 LYS cc_start: 0.8407 (pttt) cc_final: 0.8175 (pttt) REVERT: A 310 GLN cc_start: 0.8529 (mt0) cc_final: 0.8282 (mt0) REVERT: B 103 TYR cc_start: 0.8822 (m-80) cc_final: 0.8549 (m-80) REVERT: B 135 MET cc_start: 0.8913 (mmm) cc_final: 0.8528 (mmt) REVERT: B 173 ASN cc_start: 0.9054 (t0) cc_final: 0.8848 (t0) outliers start: 12 outliers final: 5 residues processed: 84 average time/residue: 0.0731 time to fit residues: 8.7451 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 : 0.301 ------------------------------------------------------------------------------- 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: 0.7980 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 43 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3754 r_free = 0.3754 target = 0.132989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098405 restraints weight = 13229.275| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.34 r_work: 0.3102 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8402 Z= 0.143 Angle : 0.584 9.274 11484 Z= 0.302 Chirality : 0.046 0.165 1342 Planarity : 0.004 0.031 1508 Dihedral : 4.468 19.545 1192 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.94 % Allowed : 6.09 % Favored : 91.97 % 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: 0.30 (0.25), residues: 1116 helix: 0.20 (0.48), residues: 127 sheet: 0.61 (0.24), residues: 423 loop : -0.01 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 226 TYR 0.014 0.001 TYR A 112 PHE 0.013 0.001 PHE A 276 TRP 0.009 0.001 TRP A 179 HIS 0.006 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8378) covalent geometry : angle 0.55208 / 0.30 (11419) SS BOND : bond 0.00178 / 0.09 ( 7) SS BOND : angle 1.64442 / 0.76 ( 14) hydrogen bonds : bond 0.03487 / 2.14 ( 317) hydrogen bonds : angle 6.10521 / 4.20 ( 813) link_ALPHA1-2 : bond 0.00664 / 0.35 ( 1) link_ALPHA1-2 : angle 1.51783 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00616 / 0.32 ( 1) link_ALPHA1-3 : angle 1.28179 / 0.79 ( 3) link_ALPHA1-6 : bond 0.00525 / 0.28 ( 1) link_ALPHA1-6 : angle 1.32367 / 1.12 ( 3) link_BETA1-4 : bond 0.01187 / 0.57 ( 6) link_BETA1-4 : angle 2.82949 / 1.74 ( 18) link_NAG-ASN : bond 0.00942 / 0.45 ( 8) link_NAG-ASN : angle 3.15390 / 2.29 ( 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: 14 poor density : 66 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8984 (t0) cc_final: 0.8263 (t0) REVERT: A 162 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8279 (t70) REVERT: A 400 MET cc_start: 0.9310 (ptm) cc_final: 0.9061 (ptm) REVERT: B 90 GLU cc_start: 0.7807 (pm20) cc_final: 0.7587 (pm20) REVERT: B 103 TYR cc_start: 0.8828 (m-80) cc_final: 0.8611 (m-10) REVERT: B 135 MET cc_start: 0.8874 (mmm) cc_final: 0.8672 (mmt) REVERT: B 173 ASN cc_start: 0.8970 (t0) cc_final: 0.8760 (t0) outliers start: 14 outliers final: 8 residues processed: 74 average time/residue: 0.0917 time to fit residues: 9.6475 Evaluate side-chains 68 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 162 ASP 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 301 VAL Chi-restraints excluded: chain B residue 320 ILE 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: 0.5980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096661 restraints weight = 13432.742| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.32 r_work: 0.3072 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8402 Z= 0.155 Angle : 0.570 9.207 11484 Z= 0.291 Chirality : 0.046 0.172 1342 Planarity : 0.004 0.032 1508 Dihedral : 4.332 16.918 1192 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.08 % Allowed : 6.93 % Favored : 91.00 % 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: 0.24 (0.25), residues: 1116 helix: 0.21 (0.49), residues: 128 sheet: 0.64 (0.24), residues: 421 loop : -0.13 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 226 TYR 0.015 0.002 TYR A 112 PHE 0.013 0.001 PHE A 326 TRP 0.012 0.001 TRP A 179 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8378) covalent geometry : angle 0.54130 / 0.29 (11419) SS BOND : bond 0.00224 / 0.11 ( 7) SS BOND : angle 1.09619 / 0.56 ( 14) hydrogen bonds : bond 0.03199 / 1.99 ( 317) hydrogen bonds : angle 5.74317 / 3.98 ( 813) link_ALPHA1-2 : bond 0.00375 / 0.20 ( 1) link_ALPHA1-2 : angle 1.39204 / 1.03 ( 3) link_ALPHA1-3 : bond 0.00675 / 0.36 ( 1) link_ALPHA1-3 : angle 1.23291 / 0.83 ( 3) link_ALPHA1-6 : bond 0.00320 / 0.17 ( 1) link_ALPHA1-6 : angle 1.47019 / 1.27 ( 3) link_BETA1-4 : bond 0.01211 / 0.59 ( 6) link_BETA1-4 : angle 2.76645 / 1.72 ( 18) link_NAG-ASN : bond 0.01140 / 0.54 ( 8) link_NAG-ASN : angle 2.97159 / 2.17 ( 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 79 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8316 (t0) cc_final: 0.8075 (t0) REVERT: A 146 ASP cc_start: 0.8963 (t0) cc_final: 0.8733 (t0) REVERT: B 90 GLU cc_start: 0.8034 (pm20) cc_final: 0.7736 (pm20) REVERT: B 103 TYR cc_start: 0.8832 (m-80) cc_final: 0.8605 (m-80) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.0911 time to fit residues: 9.3788 Evaluate side-chains 69 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 320 ILE Chi-restraints excluded: chain B residue 350 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: 1.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3730 r_free = 0.3730 target = 0.130999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.096099 restraints weight = 13386.807| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.38 r_work: 0.3062 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8402 Z= 0.149 Angle : 0.556 9.017 11484 Z= 0.284 Chirality : 0.046 0.167 1342 Planarity : 0.004 0.032 1508 Dihedral : 4.202 15.396 1192 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.22 % Allowed : 7.48 % Favored : 90.30 % 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: 0.30 (0.25), residues: 1116 helix: 0.21 (0.49), residues: 129 sheet: 0.76 (0.24), residues: 420 loop : -0.16 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 245 TYR 0.014 0.001 TYR A 112 PHE 0.013 0.001 PHE A 276 TRP 0.008 0.001 TRP A 179 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8378) covalent geometry : angle 0.52883 / 0.28 (11419) SS BOND : bond 0.00243 / 0.11 ( 7) SS BOND : angle 0.90900 / 0.43 ( 14) hydrogen bonds : bond 0.03064 / 1.90 ( 317) hydrogen bonds : angle 5.60293 / 3.89 ( 813) link_ALPHA1-2 : bond 0.00433 / 0.23 ( 1) link_ALPHA1-2 : angle 1.37742 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00695 / 0.37 ( 1) link_ALPHA1-3 : angle 1.21854 / 0.87 ( 3) link_ALPHA1-6 : bond 0.00368 / 0.19 ( 1) link_ALPHA1-6 : angle 1.40624 / 1.21 ( 3) link_BETA1-4 : bond 0.01163 / 0.56 ( 6) link_BETA1-4 : angle 2.68360 / 1.66 ( 18) link_NAG-ASN : bond 0.01068 / 0.51 ( 8) link_NAG-ASN : angle 2.86077 / 2.04 ( 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 80 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8170 (t0) cc_final: 0.7952 (t0) REVERT: A 118 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7861 (ptt) REVERT: B 90 GLU cc_start: 0.8075 (pm20) cc_final: 0.7729 (pm20) REVERT: B 103 TYR cc_start: 0.8862 (m-80) cc_final: 0.8571 (m-80) REVERT: B 355 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8130 (tp-100) REVERT: B 371 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7020 (mmmt) outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 0.0978 time to fit residues: 9.8504 Evaluate side-chains 73 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 118 MET 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 94 MET 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: 0.9990 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3719 r_free = 0.3719 target = 0.130150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095416 restraints weight = 13222.369| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.32 r_work: 0.3052 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8402 Z= 0.165 Angle : 0.557 9.057 11484 Z= 0.283 Chirality : 0.046 0.158 1342 Planarity : 0.004 0.032 1508 Dihedral : 4.219 14.863 1192 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.94 % Allowed : 8.31 % 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: 0.20 (0.25), residues: 1116 helix: 0.15 (0.48), residues: 129 sheet: 0.75 (0.24), residues: 415 loop : -0.27 (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 0.013 0.001 PHE A 276 TRP 0.008 0.002 TRP A 179 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8378) covalent geometry : angle 0.53108 / 0.28 (11419) SS BOND : bond 0.00254 / 0.12 ( 7) SS BOND : angle 0.89415 / 0.43 ( 14) hydrogen bonds : bond 0.03056 / 1.91 ( 317) hydrogen bonds : angle 5.56074 / 3.86 ( 813) link_ALPHA1-2 : bond 0.00409 / 0.22 ( 1) link_ALPHA1-2 : angle 1.35450 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00730 / 0.38 ( 1) link_ALPHA1-3 : angle 1.20015 / 0.85 ( 3) link_ALPHA1-6 : bond 0.00273 / 0.14 ( 1) link_ALPHA1-6 : angle 1.48191 / 1.29 ( 3) link_BETA1-4 : bond 0.01128 / 0.55 ( 6) link_BETA1-4 : angle 2.66778 / 1.65 ( 18) link_NAG-ASN : bond 0.01206 / 0.57 ( 8) link_NAG-ASN : angle 2.78702 / 2.04 ( 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 83 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8154 (t0) cc_final: 0.7947 (t0) REVERT: A 118 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7825 (ptt) REVERT: A 379 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7649 (mtt-85) REVERT: B 103 TYR cc_start: 0.8994 (m-80) cc_final: 0.8561 (m-80) REVERT: B 218 MET cc_start: 0.9214 (mtp) cc_final: 0.8988 (mtm) REVERT: B 355 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8175 (tp-100) REVERT: B 371 LYS cc_start: 0.7430 (mmtt) cc_final: 0.7050 (mmmt) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 0.0887 time to fit residues: 9.5462 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 : 0.387 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094042 restraints weight = 13495.194| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.31 r_work: 0.3031 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8402 Z= 0.205 Angle : 0.592 9.280 11484 Z= 0.302 Chirality : 0.047 0.169 1342 Planarity : 0.004 0.037 1508 Dihedral : 4.321 15.600 1192 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.08 % Allowed : 9.14 % Favored : 88.78 % 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: 0.06 (0.24), residues: 1116 helix: 0.04 (0.48), residues: 128 sheet: 0.72 (0.24), residues: 413 loop : -0.42 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 303 TYR 0.017 0.002 TYR A 112 PHE 0.015 0.002 PHE A 326 TRP 0.009 0.002 TRP A 179 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 8378) covalent geometry : angle 0.56761 / 0.30 (11419) SS BOND : bond 0.00298 / 0.14 ( 7) SS BOND : angle 0.98561 / 0.47 ( 14) hydrogen bonds : bond 0.03234 / 2.03 ( 317) hydrogen bonds : angle 5.65205 / 3.94 ( 813) link_ALPHA1-2 : bond 0.00410 / 0.22 ( 1) link_ALPHA1-2 : angle 1.31549 / 0.94 ( 3) link_ALPHA1-3 : bond 0.00709 / 0.37 ( 1) link_ALPHA1-3 : angle 1.16564 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00226 / 0.12 ( 1) link_ALPHA1-6 : angle 1.59662 / 1.38 ( 3) link_BETA1-4 : bond 0.01082 / 0.52 ( 6) link_BETA1-4 : angle 2.70636 / 1.67 ( 18) link_NAG-ASN : bond 0.01175 / 0.56 ( 8) link_NAG-ASN : angle 2.75905 / 1.99 ( 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 83 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8288 (t0) cc_final: 0.8052 (t0) REVERT: A 118 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7872 (ptt) REVERT: A 275 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8559 (t80) REVERT: A 303 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7861 (tpt-90) REVERT: B 103 TYR cc_start: 0.9100 (m-80) cc_final: 0.8592 (m-80) REVERT: B 218 MET cc_start: 0.9142 (mtp) cc_final: 0.8934 (mtm) REVERT: B 351 GLU cc_start: 0.8499 (tt0) cc_final: 0.8022 (mp0) REVERT: B 355 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8152 (tp-100) REVERT: B 371 LYS cc_start: 0.7511 (mmtt) cc_final: 0.7108 (mmmt) outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.0926 time to fit residues: 9.8193 Evaluate side-chains 74 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 69 optimal weight: 0.0030 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095799 restraints weight = 13360.651| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.31 r_work: 0.3060 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8402 Z= 0.131 Angle : 0.537 8.475 11484 Z= 0.274 Chirality : 0.045 0.175 1342 Planarity : 0.003 0.031 1508 Dihedral : 4.120 14.457 1192 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.08 % Allowed : 9.14 % Favored : 88.78 % 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: 0.24 (0.25), residues: 1116 helix: 0.54 (0.50), residues: 122 sheet: 0.79 (0.24), residues: 415 loop : -0.33 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.012 0.001 TYR A 112 PHE 0.011 0.001 PHE A 276 TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8378) covalent geometry : angle 0.51315 / 0.27 (11419) SS BOND : bond 0.00227 / 0.11 ( 7) SS BOND : angle 0.74844 / 0.36 ( 14) hydrogen bonds : bond 0.02843 / 1.78 ( 317) hydrogen bonds : angle 5.45963 / 3.79 ( 813) link_ALPHA1-2 : bond 0.00380 / 0.20 ( 1) link_ALPHA1-2 : angle 1.35636 / 1.01 ( 3) link_ALPHA1-3 : bond 0.00583 / 0.31 ( 1) link_ALPHA1-3 : angle 1.15965 / 0.87 ( 3) link_ALPHA1-6 : bond 0.00344 / 0.18 ( 1) link_ALPHA1-6 : angle 1.32032 / 1.15 ( 3) link_BETA1-4 : bond 0.01030 / 0.50 ( 6) link_BETA1-4 : angle 2.54756 / 1.59 ( 18) link_NAG-ASN : bond 0.00991 / 0.48 ( 8) link_NAG-ASN : angle 2.62219 / 1.94 ( 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 83 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8237 (t0) cc_final: 0.7976 (t0) REVERT: A 118 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7893 (ptt) REVERT: A 275 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8531 (t80) REVERT: A 379 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7693 (mtt-85) REVERT: B 103 TYR cc_start: 0.9027 (m-80) cc_final: 0.8636 (m-80) REVERT: B 218 MET cc_start: 0.9193 (mtp) cc_final: 0.8935 (mtm) REVERT: B 355 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8137 (tp-100) REVERT: B 371 LYS cc_start: 0.7462 (mmtt) cc_final: 0.7081 (mmmt) outliers start: 15 outliers final: 7 residues processed: 76 average time/residue: 0.1050 time to fit residues: 10.9920 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 : 0.331 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 0.0030 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3734 r_free = 0.3734 target = 0.131247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096586 restraints weight = 13286.486| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.31 r_work: 0.3092 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8402 Z= 0.122 Angle : 0.531 8.319 11484 Z= 0.271 Chirality : 0.045 0.210 1342 Planarity : 0.004 0.031 1508 Dihedral : 4.028 14.394 1192 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.80 % Allowed : 9.42 % Favored : 88.78 % 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: 0.31 (0.25), residues: 1116 helix: 0.73 (0.51), residues: 121 sheet: 0.83 (0.25), residues: 415 loop : -0.33 (0.26), residues: 580 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 0.007 0.001 TRP A 179 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8378) covalent geometry : angle 0.50849 / 0.27 (11419) SS BOND : bond 0.00198 / 0.09 ( 7) SS BOND : angle 0.66824 / 0.33 ( 14) hydrogen bonds : bond 0.02760 / 1.71 ( 317) hydrogen bonds : angle 5.34080 / 3.70 ( 813) link_ALPHA1-2 : bond 0.00382 / 0.20 ( 1) link_ALPHA1-2 : angle 1.36538 / 1.04 ( 3) link_ALPHA1-3 : bond 0.00644 / 0.34 ( 1) link_ALPHA1-3 : angle 1.23203 / 0.95 ( 3) link_ALPHA1-6 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-6 : angle 1.38686 / 1.21 ( 3) link_BETA1-4 : bond 0.01099 / 0.53 ( 6) link_BETA1-4 : angle 2.49199 / 1.55 ( 18) link_NAG-ASN : bond 0.01167 / 0.56 ( 8) link_NAG-ASN : angle 2.55655 / 1.92 ( 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 87 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8277 (t0) cc_final: 0.8028 (t0) REVERT: A 118 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7890 (ptt) REVERT: A 275 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8496 (t80) REVERT: A 379 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7834 (mtt-85) REVERT: B 103 TYR cc_start: 0.9023 (m-80) cc_final: 0.8580 (m-80) REVERT: B 268 LYS cc_start: 0.6893 (ttmm) cc_final: 0.6549 (mttp) REVERT: B 351 GLU cc_start: 0.8426 (tt0) cc_final: 0.7947 (mp0) REVERT: B 355 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8273 (tp-100) REVERT: B 371 LYS cc_start: 0.7473 (mmtt) cc_final: 0.7097 (mmmt) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.1080 time to fit residues: 11.6385 Evaluate side-chains 77 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 B residue 94 MET Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 87 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.130658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095988 restraints weight = 13255.265| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.30 r_work: 0.3079 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8402 Z= 0.144 Angle : 0.550 8.474 11484 Z= 0.279 Chirality : 0.046 0.170 1342 Planarity : 0.004 0.031 1508 Dihedral : 4.074 14.226 1192 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.52 % Allowed : 9.83 % 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: 0.28 (0.25), residues: 1116 helix: 0.71 (0.51), residues: 121 sheet: 0.79 (0.24), residues: 415 loop : -0.33 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 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/Z covalent geometry : bond 0.00328 / 0.14 ( 8378) covalent geometry : angle 0.52725 / 0.27 (11419) SS BOND : bond 0.00232 / 0.11 ( 7) SS BOND : angle 0.71290 / 0.35 ( 14) hydrogen bonds : bond 0.02884 / 1.80 ( 317) hydrogen bonds : angle 5.36405 / 3.72 ( 813) link_ALPHA1-2 : bond 0.00403 / 0.21 ( 1) link_ALPHA1-2 : angle 1.33810 / 1.01 ( 3) link_ALPHA1-3 : bond 0.00670 / 0.35 ( 1) link_ALPHA1-3 : angle 1.22462 / 0.93 ( 3) link_ALPHA1-6 : bond 0.00296 / 0.16 ( 1) link_ALPHA1-6 : angle 1.44508 / 1.26 ( 3) link_BETA1-4 : bond 0.01068 / 0.52 ( 6) link_BETA1-4 : angle 2.47389 / 1.54 ( 18) link_NAG-ASN : bond 0.01334 / 0.64 ( 8) link_NAG-ASN : angle 2.66007 / 1.98 ( 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 77 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8274 (t0) cc_final: 0.8028 (t0) REVERT: A 118 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8001 (ptt) REVERT: A 275 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8537 (t80) REVERT: A 379 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7823 (mtt-85) REVERT: B 103 TYR cc_start: 0.9060 (m-80) cc_final: 0.8600 (m-80) REVERT: B 268 LYS cc_start: 0.6875 (ttmm) cc_final: 0.6521 (mttp) REVERT: B 355 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8261 (tp-100) REVERT: B 371 LYS cc_start: 0.7500 (mmtt) cc_final: 0.7086 (mmmt) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1065 time to fit residues: 10.1002 Evaluate side-chains 74 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 B residue 94 MET Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 45 optimal weight: 40.0000 chunk 97 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3682 r_free = 0.3682 target = 0.127425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.093401 restraints weight = 13488.213| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.31 r_work: 0.3003 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8402 Z= 0.265 Angle : 0.644 9.541 11484 Z= 0.326 Chirality : 0.049 0.173 1342 Planarity : 0.004 0.041 1508 Dihedral : 4.436 16.026 1192 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.94 % Allowed : 9.83 % Favored : 88.23 % 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 (0.24), residues: 1116 helix: 0.38 (0.50), residues: 119 sheet: 0.60 (0.24), residues: 407 loop : -0.46 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 303 TYR 0.020 0.002 TYR A 112 PHE 0.018 0.002 PHE A 326 TRP 0.011 0.002 TRP A 179 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 ( 8378) covalent geometry : angle 0.62110 / 0.32 (11419) SS BOND : bond 0.00375 / 0.18 ( 7) SS BOND : angle 1.09271 / 0.53 ( 14) hydrogen bonds : bond 0.03435 / 2.17 ( 317) hydrogen bonds : angle 5.72821 / 3.99 ( 813) link_ALPHA1-2 : bond 0.00427 / 0.22 ( 1) link_ALPHA1-2 : angle 1.26803 / 0.91 ( 3) link_ALPHA1-3 : bond 0.00886 / 0.47 ( 1) link_ALPHA1-3 : angle 1.20598 / 0.80 ( 3) link_ALPHA1-6 : bond 0.00092 / 0.05 ( 1) link_ALPHA1-6 : angle 1.76700 / 1.55 ( 3) link_BETA1-4 : bond 0.01032 / 0.49 ( 6) link_BETA1-4 : angle 2.78350 / 1.71 ( 18) link_NAG-ASN : bond 0.01409 / 0.67 ( 8) link_NAG-ASN : angle 2.78428 / 2.04 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.30 seconds wall clock time: 36 minutes 39.04 seconds (2199.04 seconds total)