Starting phenix.real_space_refine on Thu Mar 13 00:46:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uja_20794/03_2025/6uja_20794.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uja_20794/03_2025/6uja_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_2025/6uja_20794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uja_20794/03_2025/6uja_20794.map" model { file = "/net/cci-nas-00/data/ceres_data/6uja_20794/03_2025/6uja_20794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uja_20794/03_2025/6uja_20794.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} 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: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 14} 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: 5.37, per 1000 atoms: 0.65 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: 2.26 Conformation dependent library (CDL) restraints added in 970.5 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: 1.13 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: 2.57 Time building geometry restraints manager: 2.59 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: 1.440 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- 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 0.083 8378 Z= 0.954 Angle : 1.487 40.507 11419 Z= 0.986 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (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 TRP 0.023 0.007 TRP B 230 HIS 0.006 0.002 HIS B 63 PHE 0.026 0.004 PHE A 276 TYR 0.043 0.006 TYR B 172 ARG 0.004 0.001 ARG B 231 *********************** 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 : 0.929 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: 0.7765 (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: 0.2858 time to fit residues: 48.8328 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 : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098822 restraints weight = 13168.368| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.30 r_work: 0.3105 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8378 Z= 0.328 Angle : 0.660 8.518 11419 Z= 0.357 Chirality : 0.048 0.192 1342 Planarity : 0.004 0.032 1508 Dihedral : 8.075 86.998 1541 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.69 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 6.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1116 helix: -0.11 (0.45), residues: 126 sheet: 0.87 (0.24), residues: 407 loop : -0.00 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 179 HIS 0.004 0.001 HIS A 113 PHE 0.018 0.002 PHE A 276 TYR 0.017 0.002 TYR A 112 ARG 0.007 0.001 ARG D 226 *********************** 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 83 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.9025 (t0) cc_final: 0.8278 (t0) REVERT: A 165 LYS cc_start: 0.8404 (pttt) cc_final: 0.8181 (pttt) REVERT: A 310 GLN cc_start: 0.8530 (mt0) cc_final: 0.8299 (mt0) REVERT: B 103 TYR cc_start: 0.8824 (m-80) cc_final: 0.8579 (m-80) REVERT: B 135 MET cc_start: 0.8896 (mmm) cc_final: 0.8498 (mmt) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 0.2176 time to fit residues: 24.5425 Evaluate side-chains 65 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 81 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.132888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098150 restraints weight = 13366.598| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.37 r_work: 0.3095 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8378 Z= 0.213 Angle : 0.554 5.318 11419 Z= 0.296 Chirality : 0.047 0.238 1342 Planarity : 0.004 0.033 1508 Dihedral : 7.036 74.164 1541 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.08 % Allowed : 6.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1116 helix: 0.20 (0.48), residues: 127 sheet: 0.57 (0.24), residues: 422 loop : -0.00 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.008 0.001 HIS B 422 PHE 0.013 0.001 PHE A 276 TYR 0.014 0.002 TYR A 112 ARG 0.006 0.001 ARG D 226 *********************** 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 79 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.9022 (t0) cc_final: 0.8804 (t0) REVERT: A 162 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8289 (t70) REVERT: A 400 MET cc_start: 0.9317 (ptm) cc_final: 0.9107 (ptm) REVERT: B 103 TYR cc_start: 0.8853 (m-80) cc_final: 0.8557 (m-80) REVERT: D 224 MET cc_start: 0.8874 (mmm) cc_final: 0.8160 (mtt) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.2025 time to fit residues: 21.0472 Evaluate side-chains 66 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 78 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 0.0670 overall best weight: 0.3518 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.133277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098452 restraints weight = 13162.386| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.34 r_work: 0.3103 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8378 Z= 0.174 Angle : 0.515 5.594 11419 Z= 0.272 Chirality : 0.046 0.255 1342 Planarity : 0.004 0.035 1508 Dihedral : 6.432 65.159 1541 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.39 % Allowed : 8.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1116 helix: 0.30 (0.49), residues: 129 sheet: 0.75 (0.24), residues: 421 loop : -0.10 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.005 0.001 HIS D 222 PHE 0.011 0.001 PHE A 276 TYR 0.012 0.001 TYR B 103 ARG 0.004 0.000 ARG D 226 *********************** 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 72 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7989 (t0) cc_final: 0.7708 (t0) REVERT: A 146 ASP cc_start: 0.8967 (t0) cc_final: 0.8738 (t0) REVERT: B 103 TYR cc_start: 0.8845 (m-80) cc_final: 0.8597 (m-10) REVERT: D 224 MET cc_start: 0.8852 (mmm) cc_final: 0.8182 (mtt) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 0.2061 time to fit residues: 19.5178 Evaluate side-chains 64 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 378 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 36 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 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 = 0.3718 r_free = 0.3718 target = 0.130268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095574 restraints weight = 13167.834| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.35 r_work: 0.3049 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8378 Z= 0.277 Angle : 0.558 6.666 11419 Z= 0.292 Chirality : 0.047 0.260 1342 Planarity : 0.004 0.038 1508 Dihedral : 6.350 59.363 1541 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.35 % Allowed : 7.48 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1116 helix: 0.24 (0.49), residues: 129 sheet: 0.73 (0.24), residues: 418 loop : -0.20 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 179 HIS 0.005 0.001 HIS B 161 PHE 0.015 0.002 PHE A 326 TYR 0.016 0.002 TYR A 112 ARG 0.004 0.001 ARG A 245 *********************** 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 81 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8254 (t0) cc_final: 0.7953 (t0) REVERT: A 118 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7870 (ptt) REVERT: B 103 TYR cc_start: 0.8923 (m-80) cc_final: 0.8641 (m-80) REVERT: B 355 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8169 (tp-100) REVERT: B 371 LYS cc_start: 0.7466 (mmtt) cc_final: 0.7077 (mmmt) REVERT: D 224 MET cc_start: 0.8858 (mmm) cc_final: 0.8156 (mtt) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 0.2664 time to fit residues: 27.5155 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 : 0.917 ------------------------------------------------------------------------------- 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 135 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 21 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.130152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.095386 restraints weight = 13201.076| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.30 r_work: 0.3053 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8378 Z= 0.254 Angle : 0.533 5.895 11419 Z= 0.279 Chirality : 0.047 0.261 1342 Planarity : 0.004 0.034 1508 Dihedral : 6.204 55.516 1541 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.08 % Allowed : 8.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1116 helix: 0.18 (0.49), residues: 129 sheet: 0.74 (0.24), residues: 414 loop : -0.26 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 179 HIS 0.004 0.001 HIS B 161 PHE 0.013 0.001 PHE A 276 TYR 0.014 0.001 TYR A 112 ARG 0.003 0.000 ARG A 245 *********************** 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 82 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8253 (t0) cc_final: 0.7906 (t0) REVERT: A 379 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7641 (mtt-85) REVERT: B 103 TYR cc_start: 0.8957 (m-80) cc_final: 0.8602 (m-80) REVERT: B 355 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8202 (tp-100) REVERT: B 371 LYS cc_start: 0.7437 (mmtt) cc_final: 0.7050 (mmmt) REVERT: D 224 MET cc_start: 0.8845 (mmm) cc_final: 0.8163 (mtt) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.2768 time to fit residues: 29.9179 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 : 0.924 ------------------------------------------------------------------------------- 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 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 135 MET 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 106 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** 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 = 0.3708 r_free = 0.3708 target = 0.129344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094569 restraints weight = 13204.254| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.30 r_work: 0.3041 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8378 Z= 0.289 Angle : 0.553 6.159 11419 Z= 0.289 Chirality : 0.047 0.255 1342 Planarity : 0.004 0.035 1508 Dihedral : 6.202 52.159 1541 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.22 % Allowed : 8.73 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1116 helix: 0.27 (0.49), residues: 126 sheet: 0.73 (0.24), residues: 411 loop : -0.37 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 179 HIS 0.005 0.001 HIS B 161 PHE 0.015 0.002 PHE A 276 TYR 0.016 0.002 TYR A 112 ARG 0.005 0.000 ARG A 245 *********************** 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 81 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8311 (t0) cc_final: 0.8055 (t0) REVERT: A 118 MET cc_start: 0.8221 (ptm) cc_final: 0.7895 (ptt) REVERT: B 103 TYR cc_start: 0.9100 (m-80) cc_final: 0.8707 (m-80) REVERT: B 320 ILE cc_start: 0.8860 (tp) cc_final: 0.8392 (pt) REVERT: B 351 GLU cc_start: 0.8372 (tt0) cc_final: 0.7932 (mp0) REVERT: B 355 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8203 (tp-100) REVERT: B 371 LYS cc_start: 0.7518 (mmtt) cc_final: 0.7120 (mmmt) REVERT: D 224 MET cc_start: 0.8725 (mmm) cc_final: 0.8109 (mtt) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.2412 time to fit residues: 24.9936 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 : 1.236 ------------------------------------------------------------------------------- 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 135 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 54 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** 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 = 0.3705 r_free = 0.3705 target = 0.129125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094203 restraints weight = 13454.749| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.32 r_work: 0.3035 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8378 Z= 0.278 Angle : 0.546 6.207 11419 Z= 0.285 Chirality : 0.047 0.248 1342 Planarity : 0.004 0.031 1508 Dihedral : 6.167 53.311 1541 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.49 % Allowed : 8.59 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1116 helix: 0.27 (0.49), residues: 126 sheet: 0.73 (0.24), residues: 413 loop : -0.39 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 230 HIS 0.003 0.001 HIS B 161 PHE 0.013 0.002 PHE A 276 TYR 0.015 0.002 TYR A 112 ARG 0.004 0.000 ARG A 379 *********************** 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: 18 poor density : 65 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8291 (t0) cc_final: 0.8049 (t0) REVERT: A 118 MET cc_start: 0.8294 (ptm) cc_final: 0.8000 (ptt) REVERT: A 379 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7530 (mtt-85) REVERT: B 103 TYR cc_start: 0.9101 (m-80) cc_final: 0.8585 (m-80) REVERT: B 320 ILE cc_start: 0.8867 (tp) cc_final: 0.8493 (pt) REVERT: B 351 GLU cc_start: 0.8517 (tt0) cc_final: 0.8020 (mp0) REVERT: B 355 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8200 (tp-100) REVERT: B 371 LYS cc_start: 0.7520 (mmtt) cc_final: 0.7120 (mmmt) REVERT: D 224 MET cc_start: 0.8706 (mmm) cc_final: 0.8081 (mtt) outliers start: 18 outliers final: 9 residues processed: 76 average time/residue: 0.2978 time to fit residues: 32.7918 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 : 1.049 ------------------------------------------------------------------------------- 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 135 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094662 restraints weight = 13464.267| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.30 r_work: 0.3046 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8378 Z= 0.254 Angle : 0.545 6.902 11419 Z= 0.284 Chirality : 0.047 0.242 1342 Planarity : 0.004 0.039 1508 Dihedral : 6.093 53.800 1541 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.94 % Allowed : 9.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1116 helix: 0.58 (0.51), residues: 120 sheet: 0.77 (0.25), residues: 407 loop : -0.42 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 179 HIS 0.003 0.001 HIS B 161 PHE 0.013 0.001 PHE A 276 TYR 0.014 0.001 TYR A 112 ARG 0.003 0.000 ARG A 245 *********************** 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 80 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8267 (t0) cc_final: 0.8040 (t0) REVERT: A 275 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8497 (t80) REVERT: B 103 TYR cc_start: 0.9096 (m-80) cc_final: 0.8601 (m-80) REVERT: B 268 LYS cc_start: 0.6948 (ttmm) cc_final: 0.6592 (mttp) REVERT: B 320 ILE cc_start: 0.8867 (tp) cc_final: 0.8507 (pt) REVERT: B 355 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8234 (tp-100) REVERT: B 371 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7079 (mmmt) REVERT: D 224 MET cc_start: 0.8694 (mmm) cc_final: 0.8113 (mtt) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.3090 time to fit residues: 30.3605 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 : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.0270 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096052 restraints weight = 13187.260| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.29 r_work: 0.3077 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8378 Z= 0.193 Angle : 0.525 7.204 11419 Z= 0.274 Chirality : 0.046 0.238 1342 Planarity : 0.004 0.036 1508 Dihedral : 5.909 51.647 1541 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.39 % Allowed : 9.70 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1116 helix: 0.73 (0.51), residues: 120 sheet: 0.79 (0.25), residues: 414 loop : -0.37 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.002 0.001 HIS B 161 PHE 0.011 0.001 PHE A 276 TYR 0.012 0.001 TYR A 112 ARG 0.003 0.000 ARG B 133 ********************** 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 79 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8282 (t0) cc_final: 0.8080 (t0) REVERT: A 275 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8499 (t80) REVERT: B 103 TYR cc_start: 0.9062 (m-80) cc_final: 0.8511 (m-80) REVERT: B 268 LYS cc_start: 0.6859 (ttmm) cc_final: 0.6511 (mttp) REVERT: B 320 ILE cc_start: 0.8893 (tp) cc_final: 0.8529 (pt) REVERT: B 355 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8285 (tp-100) REVERT: B 371 LYS cc_start: 0.7499 (mmtt) cc_final: 0.7065 (mmmt) REVERT: D 224 MET cc_start: 0.8569 (mmm) cc_final: 0.7975 (mtt) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.2521 time to fit residues: 25.1358 Evaluate side-chains 72 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 MET 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 96 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.0030 chunk 105 optimal weight: 1.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093707 restraints weight = 13519.954| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.38 r_work: 0.3020 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8378 Z= 0.317 Angle : 0.575 6.684 11419 Z= 0.298 Chirality : 0.048 0.233 1342 Planarity : 0.004 0.047 1508 Dihedral : 6.162 57.791 1541 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.39 % Allowed : 10.11 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1116 helix: 0.27 (0.49), residues: 126 sheet: 0.69 (0.25), residues: 407 loop : -0.48 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 179 HIS 0.004 0.001 HIS B 161 PHE 0.015 0.002 PHE A 276 TYR 0.017 0.002 TYR A 112 ARG 0.005 0.001 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.40 seconds wall clock time: 77 minutes 39.77 seconds (4659.77 seconds total)