Starting phenix.real_space_refine on Thu Jul 2 02:53:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oix_12935/07_2026/7oix_12935.map" } resolution = 3.6 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= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3814 2.51 5 N 937 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5869 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2097 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 21, 'TRANS': 243} Chain: "B" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3558 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.35, per 1000 atoms: 0.23 Number of scatterers: 5869 At special positions: 0 Unit cell: (68.376, 74.888, 135.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1084 8.00 N 937 7.00 C 3814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 460 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 6 " " MAN D 6 " - " MAN D 7 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 601 " - " ASN A 146 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 220 " " NAG A 604 " - " ASN A 247 " " NAG A 605 " - " ASN A 241 " " NAG C 1 " - " ASN A 177 " " NAG D 1 " - " ASN A 312 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 290.3 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 57.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.624A pdb=" N THR A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 153 through 156 Processing helix chain 'A' and resid 192 through 196 removed outlier: 4.225A pdb=" N ARG A 196 " --> pdb=" O CYS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.693A pdb=" N ALA A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 Processing helix chain 'B' and resid 52 through 73 removed outlier: 4.436A pdb=" N TYR B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLN B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 107 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 115 through 135 removed outlier: 3.855A pdb=" N ILE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.927A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 173 removed outlier: 4.240A pdb=" N TRP B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 4.393A pdb=" N THR B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N MET B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 206 Processing helix chain 'B' and resid 234 through 264 removed outlier: 3.957A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 292 through 322 removed outlier: 3.917A pdb=" N PHE B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 353 Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 357 through 373 removed outlier: 4.134A pdb=" N ALA B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Proline residue: B 369 - end of helix Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 380 through 417 Proline residue: B 402 - end of helix removed outlier: 3.842A pdb=" N LEU B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Proline residue: B 407 - end of helix Processing helix chain 'B' and resid 423 through 453 removed outlier: 4.114A pdb=" N PHE B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 489 removed outlier: 3.951A pdb=" N LYS B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Proline residue: B 478 - end of helix Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.621A pdb=" N LYS B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 78 removed outlier: 6.999A pdb=" N GLY A 268 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS A 285 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR A 266 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78 removed outlier: 3.682A pdb=" N THR A 290 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 136 removed outlier: 6.453A pdb=" N THR A 135 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR A 316 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE A 319 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE A 125 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA A 123 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR A 148 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ILE A 125 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N THR A 150 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N VAL A 127 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N ASP A 152 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA A 129 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 177 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 136 removed outlier: 6.453A pdb=" N THR A 135 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR A 316 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 217 318 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1743 1.34 - 1.46: 1525 1.46 - 1.58: 2713 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 6029 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1 MAN D 5 " pdb=" C2 MAN D 5 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C2 BMA D 3 " pdb=" C3 BMA D 3 " ideal model delta sigma weight residual 1.544 1.502 0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 6024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 7737 2.02 - 4.05: 378 4.05 - 6.07: 73 6.07 - 8.09: 20 8.09 - 10.11: 12 Bond angle restraints: 8220 Sorted by residual: angle pdb=" C LEU B 376 " pdb=" N MET B 377 " pdb=" CA MET B 377 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C ALA A 246 " pdb=" N ASN A 247 " pdb=" CA ASN A 247 " ideal model delta sigma weight residual 121.85 129.21 -7.36 1.77e+00 3.19e-01 1.73e+01 angle pdb=" CG ARG B 111 " pdb=" CD ARG B 111 " pdb=" NE ARG B 111 " ideal model delta sigma weight residual 112.00 121.12 -9.12 2.20e+00 2.07e-01 1.72e+01 angle pdb=" N GLY B 263 " pdb=" CA GLY B 263 " pdb=" C GLY B 263 " ideal model delta sigma weight residual 113.18 122.79 -9.61 2.37e+00 1.78e-01 1.64e+01 angle pdb=" CB ARG B 353 " pdb=" CG ARG B 353 " pdb=" CD ARG B 353 " ideal model delta sigma weight residual 111.30 119.90 -8.60 2.30e+00 1.89e-01 1.40e+01 ... (remaining 8215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3049 17.78 - 35.55: 293 35.55 - 53.33: 53 53.33 - 71.11: 7 71.11 - 88.88: 9 Dihedral angle restraints: 3411 sinusoidal: 1327 harmonic: 2084 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 -179.48 -87.52 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 145 " pdb=" CB CYS A 145 " ideal model delta sinusoidal sigma weight residual 93.00 33.80 59.20 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N ALA B 75 " pdb=" CA ALA B 75 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 880 0.092 - 0.183: 102 0.183 - 0.275: 4 0.275 - 0.366: 1 0.366 - 0.457: 2 Chirality restraints: 989 Sorted by residual: chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 220 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA ASN B 380 " pdb=" N ASN B 380 " pdb=" C ASN B 380 " pdb=" CB ASN B 380 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 986 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 477 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO B 478 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " -0.016 2.00e-02 2.50e+03 1.52e-02 4.65e+00 pdb=" CG TYR A 299 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 118 " 0.017 2.00e-02 2.50e+03 1.26e-02 4.00e+00 pdb=" CG TRP B 118 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 118 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 118 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 118 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 118 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 118 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 118 " 0.004 2.00e-02 2.50e+03 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 167 2.69 - 3.24: 6183 3.24 - 3.79: 9472 3.79 - 4.35: 11177 4.35 - 4.90: 19019 Nonbonded interactions: 46018 Sorted by model distance: nonbonded pdb=" OH TYR B 70 " pdb=" O TRP B 134 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR B 49 " pdb=" OG1 THR B 169 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 198 " pdb=" OE1 GLN A 250 " model vdw 2.286 3.040 nonbonded pdb=" O GLN B 462 " pdb=" NZ LYS B 467 " model vdw 2.297 3.120 nonbonded pdb=" O4 NAG C 2 " pdb=" O5 BMA C 3 " model vdw 2.312 3.040 ... (remaining 46013 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 9.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.290 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 : 0.007 0.096 6051 Z= 0.327 Angle : 1.105 10.113 8281 Z= 0.552 Chirality : 0.060 0.457 989 Planarity : 0.007 0.057 1004 Dihedral : 14.524 88.883 2052 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.97 % Allowed : 8.86 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.28), residues: 710 helix: 0.08 (0.24), residues: 368 sheet: 0.41 (0.56), residues: 80 loop : -2.45 (0.31), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 111 TYR 0.036 0.003 TYR A 299 PHE 0.023 0.003 PHE B 135 TRP 0.034 0.003 TRP B 118 HIS 0.012 0.002 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.33 ( 6029) covalent geometry : angle 1.08135 / 0.55 ( 8220) SS BOND : bond 0.00203 / 0.10 ( 5) SS BOND : angle 2.53028 / 1.18 ( 10) hydrogen bonds : bond 0.06658 / 4.62 ( 310) hydrogen bonds : angle 5.48379 / 3.85 ( 933) link_ALPHA1-2 : bond 0.00930 / 0.49 ( 1) link_ALPHA1-2 : angle 1.72327 / 0.99 ( 3) link_ALPHA1-3 : bond 0.00139 / 0.07 ( 2) link_ALPHA1-3 : angle 2.30368 / 1.36 ( 6) link_ALPHA1-6 : bond 0.00288 / 0.14 ( 3) link_ALPHA1-6 : angle 2.30118 / 1.45 ( 9) link_BETA1-4 : bond 0.00618 / 0.32 ( 3) link_BETA1-4 : angle 2.59985 / 1.58 ( 9) link_BETA1-6 : bond 0.00422 / 0.22 ( 1) link_BETA1-6 : angle 3.08986 / 1.70 ( 3) link_NAG-ASN : bond 0.00559 / 0.35 ( 7) link_NAG-ASN : angle 3.55695 / 2.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8983 (mttt) REVERT: A 99 ASP cc_start: 0.8802 (t0) cc_final: 0.8573 (t0) REVERT: A 120 MET cc_start: 0.6624 (ptm) cc_final: 0.6161 (ptp) REVERT: A 226 GLU cc_start: 0.7435 (pt0) cc_final: 0.7086 (mt-10) REVERT: A 227 TRP cc_start: 0.8124 (p90) cc_final: 0.7557 (p90) REVERT: A 262 ILE cc_start: 0.8559 (tt) cc_final: 0.8323 (tt) REVERT: A 293 LYS cc_start: 0.8707 (tttt) cc_final: 0.8488 (ttpp) REVERT: B 69 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (mt) REVERT: B 111 ARG cc_start: 0.4986 (ttm170) cc_final: 0.2973 (ttp-170) REVERT: B 155 GLU cc_start: 0.8912 (tp30) cc_final: 0.8376 (mm-30) REVERT: B 176 GLN cc_start: 0.7802 (mt0) cc_final: 0.7116 (tm-30) REVERT: B 239 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 289 MET cc_start: 0.3365 (tpt) cc_final: 0.2588 (tpt) REVERT: B 309 MET cc_start: 0.7070 (ptp) cc_final: 0.6702 (ptp) REVERT: B 370 PHE cc_start: 0.7494 (m-80) cc_final: 0.7280 (m-10) REVERT: B 377 MET cc_start: 0.1822 (ptt) cc_final: 0.1492 (ptt) REVERT: B 458 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7013 (ttm-80) outliers start: 6 outliers final: 1 residues processed: 150 average time/residue: 0.0896 time to fit residues: 17.0965 Evaluate side-chains 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 317 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 68 GLN B 235 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.133565 restraints weight = 12073.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136741 restraints weight = 5882.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138070 restraints weight = 3334.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138924 restraints weight = 2314.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139473 restraints weight = 1832.280| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6051 Z= 0.180 Angle : 0.772 7.702 8281 Z= 0.376 Chirality : 0.045 0.316 989 Planarity : 0.005 0.044 1004 Dihedral : 5.308 22.414 773 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.38 % Allowed : 16.75 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.29), residues: 710 helix: 0.90 (0.26), residues: 366 sheet: 0.29 (0.57), residues: 80 loop : -2.19 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 77 TYR 0.021 0.002 TYR A 299 PHE 0.021 0.002 PHE B 468 TRP 0.018 0.002 TRP B 146 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 6029) covalent geometry : angle 0.74934 / 0.37 ( 8220) SS BOND : bond 0.00359 / 0.25 ( 5) SS BOND : angle 1.64143 / 0.76 ( 10) hydrogen bonds : bond 0.04992 / 3.42 ( 310) hydrogen bonds : angle 4.73970 / 3.35 ( 933) link_ALPHA1-2 : bond 0.00947 / 0.50 ( 1) link_ALPHA1-2 : angle 1.79927 / 1.03 ( 3) link_ALPHA1-3 : bond 0.00315 / 0.16 ( 2) link_ALPHA1-3 : angle 1.56628 / 0.94 ( 6) link_ALPHA1-6 : bond 0.00069 / 0.03 ( 3) link_ALPHA1-6 : angle 1.53973 / 0.98 ( 9) link_BETA1-4 : bond 0.00463 / 0.24 ( 3) link_BETA1-4 : angle 2.66075 / 1.52 ( 9) link_BETA1-6 : bond 0.00594 / 0.31 ( 1) link_BETA1-6 : angle 2.88420 / 1.56 ( 3) link_NAG-ASN : bond 0.00437 / 0.29 ( 7) link_NAG-ASN : angle 2.72912 / 1.73 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8788 (t0) cc_final: 0.8585 (t0) REVERT: A 114 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: A 120 MET cc_start: 0.7204 (ptm) cc_final: 0.6940 (ptp) REVERT: A 262 ILE cc_start: 0.9085 (tt) cc_final: 0.8821 (tt) REVERT: B 111 ARG cc_start: 0.5403 (ttm170) cc_final: 0.3207 (ttm110) REVERT: B 239 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 289 MET cc_start: 0.3088 (tpt) cc_final: 0.2205 (tpt) REVERT: B 309 MET cc_start: 0.7337 (ptp) cc_final: 0.7076 (ptp) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 0.0815 time to fit residues: 13.9231 Evaluate side-chains 114 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 0.0170 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS A 287 HIS B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS B 421 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133866 restraints weight = 11885.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136497 restraints weight = 6153.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138195 restraints weight = 3747.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139312 restraints weight = 2572.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140010 restraints weight = 1925.023| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6051 Z= 0.146 Angle : 0.710 7.904 8281 Z= 0.343 Chirality : 0.044 0.293 989 Planarity : 0.005 0.075 1004 Dihedral : 5.014 21.076 769 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.70 % Allowed : 20.77 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.30), residues: 710 helix: 1.02 (0.26), residues: 365 sheet: 0.22 (0.58), residues: 80 loop : -2.09 (0.32), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.018 0.001 TYR A 299 PHE 0.020 0.001 PHE B 350 TRP 0.026 0.002 TRP B 118 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6029) covalent geometry : angle 0.69114 / 0.34 ( 8220) SS BOND : bond 0.00409 / 0.30 ( 5) SS BOND : angle 1.51259 / 0.66 ( 10) hydrogen bonds : bond 0.04639 / 3.20 ( 310) hydrogen bonds : angle 4.49040 / 3.17 ( 933) link_ALPHA1-2 : bond 0.01075 / 0.57 ( 1) link_ALPHA1-2 : angle 1.72275 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00414 / 0.21 ( 2) link_ALPHA1-3 : angle 1.50168 / 0.93 ( 6) link_ALPHA1-6 : bond 0.00208 / 0.10 ( 3) link_ALPHA1-6 : angle 1.39714 / 0.89 ( 9) link_BETA1-4 : bond 0.00458 / 0.23 ( 3) link_BETA1-4 : angle 2.33655 / 1.35 ( 9) link_BETA1-6 : bond 0.00567 / 0.30 ( 1) link_BETA1-6 : angle 2.34110 / 1.27 ( 3) link_NAG-ASN : bond 0.00340 / 0.22 ( 7) link_NAG-ASN : angle 2.42131 / 1.52 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8782 (t0) cc_final: 0.8552 (t0) REVERT: A 114 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: B 111 ARG cc_start: 0.5449 (ttm170) cc_final: 0.3434 (ttp-170) REVERT: B 187 MET cc_start: 0.8235 (mmm) cc_final: 0.8018 (mmm) REVERT: B 239 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 289 MET cc_start: 0.2942 (tpt) cc_final: 0.2026 (tpt) REVERT: B 414 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7213 (t-90) REVERT: B 431 TYR cc_start: 0.7934 (t80) cc_final: 0.7587 (t80) outliers start: 23 outliers final: 16 residues processed: 127 average time/residue: 0.0769 time to fit residues: 12.5209 Evaluate side-chains 123 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133841 restraints weight = 11982.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136475 restraints weight = 6212.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138181 restraints weight = 3802.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139306 restraints weight = 2614.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140057 restraints weight = 1965.541| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6051 Z= 0.140 Angle : 0.699 12.311 8281 Z= 0.332 Chirality : 0.042 0.256 989 Planarity : 0.005 0.080 1004 Dihedral : 4.892 20.760 769 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.51 % Allowed : 21.90 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.30), residues: 710 helix: 1.08 (0.26), residues: 365 sheet: 0.17 (0.58), residues: 80 loop : -2.09 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.014 0.001 TYR A 299 PHE 0.018 0.001 PHE B 468 TRP 0.024 0.002 TRP B 118 HIS 0.006 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6029) covalent geometry : angle 0.68096 / 0.33 ( 8220) SS BOND : bond 0.00368 / 0.27 ( 5) SS BOND : angle 1.58998 / 0.73 ( 10) hydrogen bonds : bond 0.04444 / 3.07 ( 310) hydrogen bonds : angle 4.38267 / 3.09 ( 933) link_ALPHA1-2 : bond 0.00900 / 0.47 ( 1) link_ALPHA1-2 : angle 1.59089 / 0.92 ( 3) link_ALPHA1-3 : bond 0.00347 / 0.17 ( 2) link_ALPHA1-3 : angle 1.48012 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00192 / 0.09 ( 3) link_ALPHA1-6 : angle 1.40660 / 0.89 ( 9) link_BETA1-4 : bond 0.00402 / 0.20 ( 3) link_BETA1-4 : angle 2.28288 / 1.32 ( 9) link_BETA1-6 : bond 0.00515 / 0.27 ( 1) link_BETA1-6 : angle 2.26825 / 1.23 ( 3) link_NAG-ASN : bond 0.00292 / 0.17 ( 7) link_NAG-ASN : angle 2.25132 / 1.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8764 (t0) cc_final: 0.8532 (t0) REVERT: A 114 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: B 111 ARG cc_start: 0.5581 (ttm170) cc_final: 0.2419 (ttp-170) REVERT: B 187 MET cc_start: 0.8279 (mmm) cc_final: 0.8063 (mmm) REVERT: B 237 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6795 (mt-10) REVERT: B 239 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 289 MET cc_start: 0.2924 (tpt) cc_final: 0.1989 (tpt) REVERT: B 370 PHE cc_start: 0.6619 (m-10) cc_final: 0.6401 (m-10) REVERT: B 431 TYR cc_start: 0.7970 (t80) cc_final: 0.7637 (t80) outliers start: 28 outliers final: 17 residues processed: 130 average time/residue: 0.0787 time to fit residues: 13.4922 Evaluate side-chains 120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133881 restraints weight = 12187.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136419 restraints weight = 6272.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.138137 restraints weight = 3863.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139267 restraints weight = 2662.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140005 restraints weight = 1992.182| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6051 Z= 0.143 Angle : 0.698 10.095 8281 Z= 0.333 Chirality : 0.043 0.309 989 Planarity : 0.005 0.082 1004 Dihedral : 4.846 20.909 769 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.67 % Allowed : 23.03 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.30), residues: 710 helix: 1.10 (0.26), residues: 365 sheet: 0.08 (0.58), residues: 80 loop : -2.11 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.014 0.001 TYR A 299 PHE 0.015 0.001 PHE B 468 TRP 0.022 0.002 TRP B 118 HIS 0.006 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6029) covalent geometry : angle 0.67346 / 0.33 ( 8220) SS BOND : bond 0.00227 / 0.15 ( 5) SS BOND : angle 1.96259 / 0.88 ( 10) hydrogen bonds : bond 0.04383 / 3.02 ( 310) hydrogen bonds : angle 4.35278 / 3.06 ( 933) link_ALPHA1-2 : bond 0.00671 / 0.35 ( 1) link_ALPHA1-2 : angle 1.43913 / 0.83 ( 3) link_ALPHA1-3 : bond 0.00333 / 0.16 ( 2) link_ALPHA1-3 : angle 1.46540 / 0.90 ( 6) link_ALPHA1-6 : bond 0.00178 / 0.09 ( 3) link_ALPHA1-6 : angle 1.39514 / 0.88 ( 9) link_BETA1-4 : bond 0.00398 / 0.20 ( 3) link_BETA1-4 : angle 2.27460 / 1.32 ( 9) link_BETA1-6 : bond 0.00484 / 0.25 ( 1) link_BETA1-6 : angle 2.21034 / 1.20 ( 3) link_NAG-ASN : bond 0.00323 / 0.22 ( 7) link_NAG-ASN : angle 2.86333 / 1.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8761 (t0) cc_final: 0.8520 (t0) REVERT: A 114 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: B 111 ARG cc_start: 0.5562 (ttm170) cc_final: 0.2454 (ttp-170) REVERT: B 207 GLN cc_start: 0.8341 (tp-100) cc_final: 0.8127 (tp-100) REVERT: B 237 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6840 (mt-10) REVERT: B 239 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 289 MET cc_start: 0.2909 (tpt) cc_final: 0.1976 (tpt) REVERT: B 309 MET cc_start: 0.7617 (ptp) cc_final: 0.7209 (ptp) REVERT: B 370 PHE cc_start: 0.6582 (m-10) cc_final: 0.6360 (m-10) REVERT: B 431 TYR cc_start: 0.7977 (t80) cc_final: 0.7648 (t80) outliers start: 29 outliers final: 19 residues processed: 128 average time/residue: 0.0761 time to fit residues: 12.8099 Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.145207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.133657 restraints weight = 11938.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136242 restraints weight = 6192.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137905 restraints weight = 3805.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139020 restraints weight = 2629.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139685 restraints weight = 1989.243| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6051 Z= 0.141 Angle : 0.678 8.801 8281 Z= 0.325 Chirality : 0.043 0.258 989 Planarity : 0.005 0.086 1004 Dihedral : 4.806 20.918 769 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.51 % Allowed : 23.83 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.30), residues: 710 helix: 1.15 (0.26), residues: 365 sheet: -0.03 (0.57), residues: 80 loop : -2.12 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.013 0.001 TYR A 299 PHE 0.011 0.001 PHE B 150 TRP 0.021 0.002 TRP B 118 HIS 0.002 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6029) covalent geometry : angle 0.65910 / 0.32 ( 8220) SS BOND : bond 0.00355 / 0.27 ( 5) SS BOND : angle 1.65431 / 0.76 ( 10) hydrogen bonds : bond 0.04260 / 2.91 ( 310) hydrogen bonds : angle 4.32509 / 3.05 ( 933) link_ALPHA1-2 : bond 0.00837 / 0.44 ( 1) link_ALPHA1-2 : angle 1.53738 / 0.89 ( 3) link_ALPHA1-3 : bond 0.00351 / 0.17 ( 2) link_ALPHA1-3 : angle 1.47408 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00214 / 0.11 ( 3) link_ALPHA1-6 : angle 1.40035 / 0.89 ( 9) link_BETA1-4 : bond 0.00378 / 0.19 ( 3) link_BETA1-4 : angle 2.25242 / 1.30 ( 9) link_BETA1-6 : bond 0.00459 / 0.24 ( 1) link_BETA1-6 : angle 2.14774 / 1.17 ( 3) link_NAG-ASN : bond 0.00249 / 0.14 ( 7) link_NAG-ASN : angle 2.31875 / 1.49 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8764 (t0) cc_final: 0.8509 (t0) REVERT: A 114 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: B 111 ARG cc_start: 0.5544 (ttm170) cc_final: 0.3471 (ttm110) REVERT: B 237 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6845 (mt-10) REVERT: B 239 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 289 MET cc_start: 0.2913 (tpt) cc_final: 0.1973 (tpt) REVERT: B 309 MET cc_start: 0.7543 (ptp) cc_final: 0.7203 (ptp) REVERT: B 370 PHE cc_start: 0.6585 (m-10) cc_final: 0.6366 (m-10) REVERT: B 431 TYR cc_start: 0.7945 (t80) cc_final: 0.7596 (t80) outliers start: 28 outliers final: 22 residues processed: 123 average time/residue: 0.0738 time to fit residues: 11.8930 Evaluate side-chains 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.134403 restraints weight = 11970.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136989 restraints weight = 6195.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138656 restraints weight = 3787.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139784 restraints weight = 2613.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140449 restraints weight = 1959.169| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6051 Z= 0.131 Angle : 0.680 8.476 8281 Z= 0.324 Chirality : 0.042 0.236 989 Planarity : 0.005 0.077 1004 Dihedral : 4.737 20.100 769 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.15 % Allowed : 23.67 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.30), residues: 710 helix: 1.22 (0.26), residues: 365 sheet: -0.08 (0.57), residues: 80 loop : -2.05 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.013 0.001 TYR A 299 PHE 0.014 0.001 PHE B 154 TRP 0.019 0.002 TRP B 118 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6029) covalent geometry : angle 0.66344 / 0.32 ( 8220) SS BOND : bond 0.00329 / 0.25 ( 5) SS BOND : angle 1.65042 / 0.77 ( 10) hydrogen bonds : bond 0.04172 / 2.86 ( 310) hydrogen bonds : angle 4.26183 / 3.00 ( 933) link_ALPHA1-2 : bond 0.00796 / 0.42 ( 1) link_ALPHA1-2 : angle 1.51123 / 0.87 ( 3) link_ALPHA1-3 : bond 0.00365 / 0.18 ( 2) link_ALPHA1-3 : angle 1.46223 / 0.90 ( 6) link_ALPHA1-6 : bond 0.00254 / 0.13 ( 3) link_ALPHA1-6 : angle 1.38089 / 0.87 ( 9) link_BETA1-4 : bond 0.00382 / 0.19 ( 3) link_BETA1-4 : angle 2.14824 / 1.24 ( 9) link_BETA1-6 : bond 0.00482 / 0.25 ( 1) link_BETA1-6 : angle 2.00881 / 1.10 ( 3) link_NAG-ASN : bond 0.00261 / 0.16 ( 7) link_NAG-ASN : angle 2.09745 / 1.32 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8753 (t0) cc_final: 0.8488 (t0) REVERT: A 114 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: B 68 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: B 111 ARG cc_start: 0.5570 (ttm170) cc_final: 0.2055 (ttp-110) REVERT: B 237 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6860 (mt-10) REVERT: B 239 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 289 MET cc_start: 0.2890 (tpt) cc_final: 0.1939 (tpt) REVERT: B 309 MET cc_start: 0.7470 (ptp) cc_final: 0.7252 (ptp) REVERT: B 370 PHE cc_start: 0.6563 (m-80) cc_final: 0.6268 (m-10) REVERT: B 431 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7566 (t80) outliers start: 32 outliers final: 21 residues processed: 132 average time/residue: 0.0713 time to fit residues: 12.4095 Evaluate side-chains 130 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.0030 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 34 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 overall best weight: 0.1768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** 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 = 0.3940 r_free = 0.3940 target = 0.147480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136228 restraints weight = 12009.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138774 restraints weight = 6145.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140403 restraints weight = 3751.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141421 restraints weight = 2588.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142204 restraints weight = 1970.486| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6051 Z= 0.122 Angle : 0.673 9.213 8281 Z= 0.319 Chirality : 0.041 0.275 989 Planarity : 0.005 0.070 1004 Dihedral : 4.619 18.962 769 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.38 % Allowed : 24.96 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.30), residues: 710 helix: 1.28 (0.26), residues: 365 sheet: -0.10 (0.58), residues: 80 loop : -1.96 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.012 0.001 TYR A 299 PHE 0.012 0.001 PHE B 154 TRP 0.018 0.001 TRP B 118 HIS 0.002 0.000 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6029) covalent geometry : angle 0.65667 / 0.31 ( 8220) SS BOND : bond 0.00119 / 0.06 ( 5) SS BOND : angle 2.24793 / 1.06 ( 10) hydrogen bonds : bond 0.03966 / 2.71 ( 310) hydrogen bonds : angle 4.19787 / 2.95 ( 933) link_ALPHA1-2 : bond 0.00649 / 0.34 ( 1) link_ALPHA1-2 : angle 1.44890 / 0.84 ( 3) link_ALPHA1-3 : bond 0.00417 / 0.21 ( 2) link_ALPHA1-3 : angle 1.44561 / 0.90 ( 6) link_ALPHA1-6 : bond 0.00322 / 0.16 ( 3) link_ALPHA1-6 : angle 1.38134 / 0.87 ( 9) link_BETA1-4 : bond 0.00473 / 0.24 ( 3) link_BETA1-4 : angle 2.02702 / 1.17 ( 9) link_BETA1-6 : bond 0.00522 / 0.27 ( 1) link_BETA1-6 : angle 1.72290 / 0.94 ( 3) link_NAG-ASN : bond 0.00295 / 0.18 ( 7) link_NAG-ASN : angle 1.83827 / 1.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8693 (t0) cc_final: 0.8438 (t0) REVERT: A 114 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: B 111 ARG cc_start: 0.5444 (ttm170) cc_final: 0.2475 (ttp-110) REVERT: B 237 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6832 (mt-10) REVERT: B 239 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 285 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4573 (tp) REVERT: B 289 MET cc_start: 0.2818 (tpt) cc_final: 0.1913 (tpt) REVERT: B 370 PHE cc_start: 0.6512 (m-80) cc_final: 0.6219 (m-10) REVERT: B 431 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7607 (t80) outliers start: 21 outliers final: 17 residues processed: 126 average time/residue: 0.0705 time to fit residues: 11.7604 Evaluate side-chains 128 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.144781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133068 restraints weight = 12093.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135619 restraints weight = 6312.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137263 restraints weight = 3890.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138380 restraints weight = 2708.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139134 restraints weight = 2043.435| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6051 Z= 0.163 Angle : 0.739 11.200 8281 Z= 0.350 Chirality : 0.045 0.398 989 Planarity : 0.005 0.095 1004 Dihedral : 4.781 22.256 769 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.86 % Allowed : 25.44 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.30), residues: 710 helix: 1.22 (0.26), residues: 365 sheet: -0.05 (0.59), residues: 80 loop : -2.11 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.014 0.001 TYR A 299 PHE 0.014 0.001 PHE B 154 TRP 0.020 0.002 TRP B 118 HIS 0.002 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6029) covalent geometry : angle 0.70812 / 0.34 ( 8220) SS BOND : bond 0.00254 / 0.18 ( 5) SS BOND : angle 1.97106 / 0.90 ( 10) hydrogen bonds : bond 0.04221 / 2.90 ( 310) hydrogen bonds : angle 4.32348 / 3.05 ( 933) link_ALPHA1-2 : bond 0.00763 / 0.40 ( 1) link_ALPHA1-2 : angle 1.47881 / 0.85 ( 3) link_ALPHA1-3 : bond 0.00342 / 0.17 ( 2) link_ALPHA1-3 : angle 1.52522 / 0.93 ( 6) link_ALPHA1-6 : bond 0.00279 / 0.14 ( 3) link_ALPHA1-6 : angle 1.43717 / 0.91 ( 9) link_BETA1-4 : bond 0.00275 / 0.14 ( 3) link_BETA1-4 : angle 2.26399 / 1.32 ( 9) link_BETA1-6 : bond 0.00433 / 0.23 ( 1) link_BETA1-6 : angle 2.29291 / 1.25 ( 3) link_NAG-ASN : bond 0.00351 / 0.21 ( 7) link_NAG-ASN : angle 3.50322 / 2.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8733 (t0) cc_final: 0.8475 (t0) REVERT: A 114 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: B 111 ARG cc_start: 0.5553 (ttm170) cc_final: 0.2824 (ttp-170) REVERT: B 237 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6877 (mt-10) REVERT: B 239 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 285 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4353 (tt) REVERT: B 289 MET cc_start: 0.2926 (tpt) cc_final: 0.1996 (tpt) REVERT: B 309 MET cc_start: 0.7367 (ptp) cc_final: 0.7166 (ptp) REVERT: B 370 PHE cc_start: 0.6517 (m-80) cc_final: 0.6284 (m-10) REVERT: B 431 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7593 (t80) outliers start: 24 outliers final: 16 residues processed: 125 average time/residue: 0.0665 time to fit residues: 10.9791 Evaluate side-chains 126 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.146148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134698 restraints weight = 12168.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137225 restraints weight = 6311.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138889 restraints weight = 3898.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140014 restraints weight = 2687.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140670 restraints weight = 2029.905| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6051 Z= 0.134 Angle : 0.698 9.187 8281 Z= 0.332 Chirality : 0.043 0.324 989 Planarity : 0.005 0.089 1004 Dihedral : 4.689 21.632 769 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.70 % Allowed : 25.28 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.31), residues: 710 helix: 1.24 (0.26), residues: 365 sheet: -0.03 (0.60), residues: 80 loop : -2.10 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 500 TYR 0.013 0.001 TYR A 299 PHE 0.011 0.001 PHE B 154 TRP 0.019 0.001 TRP B 118 HIS 0.003 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6029) covalent geometry : angle 0.67340 / 0.33 ( 8220) SS BOND : bond 0.00212 / 0.15 ( 5) SS BOND : angle 1.75506 / 0.81 ( 10) hydrogen bonds : bond 0.04087 / 2.79 ( 310) hydrogen bonds : angle 4.23880 / 2.99 ( 933) link_ALPHA1-2 : bond 0.00681 / 0.36 ( 1) link_ALPHA1-2 : angle 1.44526 / 0.84 ( 3) link_ALPHA1-3 : bond 0.00370 / 0.19 ( 2) link_ALPHA1-3 : angle 1.45140 / 0.90 ( 6) link_ALPHA1-6 : bond 0.00243 / 0.12 ( 3) link_ALPHA1-6 : angle 1.36915 / 0.86 ( 9) link_BETA1-4 : bond 0.00361 / 0.18 ( 3) link_BETA1-4 : angle 2.12322 / 1.23 ( 9) link_BETA1-6 : bond 0.00439 / 0.23 ( 1) link_BETA1-6 : angle 1.86774 / 1.02 ( 3) link_NAG-ASN : bond 0.00294 / 0.19 ( 7) link_NAG-ASN : angle 2.99351 / 2.18 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8724 (t0) cc_final: 0.8457 (t0) REVERT: A 114 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: A 295 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6904 (mp10) REVERT: B 68 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: B 111 ARG cc_start: 0.5564 (ttm170) cc_final: 0.2791 (ttp-170) REVERT: B 131 PHE cc_start: 0.7725 (t80) cc_final: 0.7507 (t80) REVERT: B 237 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6884 (mt-10) REVERT: B 239 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 285 LEU cc_start: 0.4976 (OUTLIER) cc_final: 0.4285 (tt) REVERT: B 289 MET cc_start: 0.2889 (tpt) cc_final: 0.1969 (tpt) REVERT: B 309 MET cc_start: 0.7327 (ptp) cc_final: 0.7100 (ptp) REVERT: B 370 PHE cc_start: 0.6510 (m-80) cc_final: 0.6229 (m-10) REVERT: B 431 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7579 (t80) outliers start: 23 outliers final: 18 residues processed: 122 average time/residue: 0.0759 time to fit residues: 12.2241 Evaluate side-chains 126 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 314 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.143514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132070 restraints weight = 12123.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.135339 restraints weight = 6446.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136558 restraints weight = 3871.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137342 restraints weight = 2521.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137653 restraints weight = 2240.722| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6051 Z= 0.198 Angle : 0.754 9.771 8281 Z= 0.360 Chirality : 0.046 0.368 989 Planarity : 0.005 0.097 1004 Dihedral : 4.861 23.126 769 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.86 % Allowed : 24.96 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.31), residues: 710 helix: 1.16 (0.26), residues: 365 sheet: -0.02 (0.60), residues: 80 loop : -2.23 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.015 0.001 TYR A 299 PHE 0.014 0.001 PHE B 468 TRP 0.019 0.002 TRP B 118 HIS 0.002 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 6029) covalent geometry : angle 0.72785 / 0.35 ( 8220) SS BOND : bond 0.00251 / 0.18 ( 5) SS BOND : angle 1.92234 / 0.88 ( 10) hydrogen bonds : bond 0.04328 / 2.95 ( 310) hydrogen bonds : angle 4.36177 / 3.08 ( 933) link_ALPHA1-2 : bond 0.00797 / 0.42 ( 1) link_ALPHA1-2 : angle 1.51007 / 0.87 ( 3) link_ALPHA1-3 : bond 0.00322 / 0.16 ( 2) link_ALPHA1-3 : angle 1.49689 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00160 / 0.08 ( 3) link_ALPHA1-6 : angle 1.44233 / 0.91 ( 9) link_BETA1-4 : bond 0.00246 / 0.12 ( 3) link_BETA1-4 : angle 2.36757 / 1.38 ( 9) link_BETA1-6 : bond 0.00329 / 0.17 ( 1) link_BETA1-6 : angle 2.33220 / 1.27 ( 3) link_NAG-ASN : bond 0.00370 / 0.19 ( 7) link_NAG-ASN : angle 3.14391 / 2.21 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1187.79 seconds wall clock time: 21 minutes 18.20 seconds (1278.20 seconds total)