Starting phenix.real_space_refine on Sun Jun 8 16:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4p_21044/06_2025/6v4p_21044.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4p_21044/06_2025/6v4p_21044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v4p_21044/06_2025/6v4p_21044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4p_21044/06_2025/6v4p_21044.map" model { file = "/net/cci-nas-00/data/ceres_data/6v4p_21044/06_2025/6v4p_21044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4p_21044/06_2025/6v4p_21044.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 41 5.16 5 C 6131 2.51 5 N 1636 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9717 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3467 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 27, 'TRANS': 424} Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2927 Classifications: {'peptide': 375} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 356} Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1665 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 6, 'TRANS': 203} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.18, per 1000 atoms: 0.64 Number of scatterers: 9717 At special positions: 0 Unit cell: (99, 150, 76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 41 16.00 Mg 1 11.99 O 1902 8.00 N 1636 7.00 C 6131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " 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 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 24 sheets defined 12.5% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.763A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.665A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.311A pdb=" N ASP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.765A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.501A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.505A pdb=" N SER C 91 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.936A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 189 removed outlier: 4.083A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 8.111A pdb=" N GLY A 63 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 10 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN A 7 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG A 449 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP A 434 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 424 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 removed outlier: 4.338A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.583A pdb=" N GLN A 82 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.748A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.521A pdb=" N GLY A 398 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.503A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB4, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.161A pdb=" N PHE B 153 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR B 195 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE B 151 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 197 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 149 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 309 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 248 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR B 311 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR B 250 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 333 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 310 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.351A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AB8, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 174 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 155 through 159 removed outlier: 4.480A pdb=" N TYR C 199 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 33 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 118 removed outlier: 4.928A pdb=" N SER D 131 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU D 181 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 147 through 150 347 hydrogen bonds defined for protein. 888 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: 3.45 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1634 1.32 - 1.44: 2738 1.44 - 1.57: 5507 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 9938 Sorted by residual: bond pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" CA ASN D 32 " pdb=" C ASN D 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.12e+01 bond pdb=" C ILE D 29 " pdb=" O ILE D 29 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" C SER D 30 " pdb=" O SER D 30 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.26e-02 6.30e+03 8.11e+00 bond pdb=" C ASN D 32 " pdb=" O ASN D 32 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.26e-02 6.30e+03 7.78e+00 ... (remaining 9933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 13420 2.70 - 5.41: 88 5.41 - 8.11: 5 8.11 - 10.81: 0 10.81 - 13.52: 1 Bond angle restraints: 13514 Sorted by residual: angle pdb=" C LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta sigma weight residual 109.61 117.10 -7.49 1.58e+00 4.01e-01 2.25e+01 angle pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " pdb=" CG LEU B 375 " ideal model delta sigma weight residual 116.30 102.78 13.52 3.50e+00 8.16e-02 1.49e+01 angle pdb=" C CYS B 374 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 121.31 126.33 -5.02 1.49e+00 4.50e-01 1.13e+01 angle pdb=" N SER D 30 " pdb=" CA SER D 30 " pdb=" C SER D 30 " ideal model delta sigma weight residual 110.80 117.64 -6.84 2.13e+00 2.20e-01 1.03e+01 angle pdb=" C ILE D 29 " pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.34e+00 ... (remaining 13509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 5514 16.69 - 33.39: 297 33.39 - 50.08: 77 50.08 - 66.77: 25 66.77 - 83.47: 9 Dihedral angle restraints: 5922 sinusoidal: 2300 harmonic: 3622 Sorted by residual: dihedral pdb=" CA LEU B 375 " pdb=" C LEU B 375 " pdb=" N ASN B 376 " pdb=" CA ASN B 376 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA THR D 39 " pdb=" C THR D 39 " pdb=" N SER D 40 " pdb=" CA SER D 40 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C LEU B 375 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta harmonic sigma weight residual -122.60 -133.94 11.34 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 5919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1328 0.073 - 0.146: 162 0.146 - 0.218: 2 0.218 - 0.291: 2 0.291 - 0.364: 2 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA LEU B 375 " pdb=" N LEU B 375 " pdb=" C LEU B 375 " pdb=" CB LEU B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU B 375 " pdb=" CB LEU B 375 " pdb=" CD1 LEU B 375 " pdb=" CD2 LEU B 375 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER D 30 " pdb=" N SER D 30 " pdb=" C SER D 30 " pdb=" CB SER D 30 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1493 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 375 " 0.019 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU B 375 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU B 375 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 376 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 29 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE D 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE D 29 " -0.015 2.00e-02 2.50e+03 pdb=" N SER D 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 153 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 154 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 154 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 209 2.65 - 3.21: 8814 3.21 - 3.77: 15823 3.77 - 4.34: 23593 4.34 - 4.90: 38440 Nonbonded interactions: 86879 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B 701 " model vdw 2.084 2.170 nonbonded pdb=" OH TYR A 288 " pdb=" OD1 ASP B 259 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS B 417 " pdb=" O PHE B 421 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR B 178 " pdb=" OD2 ASP C 57 " model vdw 2.233 3.040 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.241 3.040 ... (remaining 86874 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.900 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.005 0.046 9948 Z= 0.223 Angle : 0.601 13.516 13534 Z= 0.336 Chirality : 0.047 0.364 1496 Planarity : 0.004 0.042 1758 Dihedral : 12.282 83.466 3584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.07 % Favored : 95.69 % Rotamer: Outliers : 3.16 % Allowed : 7.72 % Favored : 89.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.21), residues: 1254 helix: -2.93 (0.33), residues: 116 sheet: -1.38 (0.22), residues: 448 loop : -1.87 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 33 HIS 0.005 0.001 HIS A 291 PHE 0.017 0.002 PHE A 19 TYR 0.014 0.002 TYR D 50 ARG 0.004 0.001 ARG B 352 Details of bonding type rmsd hydrogen bonds : bond 0.20625 ( 329) hydrogen bonds : angle 9.87975 ( 888) SS BOND : bond 0.00271 ( 10) SS BOND : angle 0.96227 ( 20) covalent geometry : bond 0.00467 ( 9938) covalent geometry : angle 0.60047 (13514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.043 Fit side-chains REVERT: A 23 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 77 ARG cc_start: 0.7045 (mpt180) cc_final: 0.6137 (ttt-90) REVERT: A 120 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 125 THR cc_start: 0.9011 (p) cc_final: 0.8534 (p) REVERT: A 166 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: A 208 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7667 (mmt180) REVERT: A 386 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7845 (mtm180) REVERT: A 401 SER cc_start: 0.8835 (p) cc_final: 0.8554 (m) REVERT: B 93 ARG cc_start: 0.7249 (ptm160) cc_final: 0.6320 (ttt180) REVERT: B 108 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7484 (pt0) REVERT: B 137 LYS cc_start: 0.8387 (mttt) cc_final: 0.7989 (mtmt) REVERT: B 187 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.7806 (tmm) REVERT: B 277 SER cc_start: 0.8844 (p) cc_final: 0.8592 (m) REVERT: B 323 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7710 (mt-10) REVERT: B 365 GLU cc_start: 0.8079 (mp0) cc_final: 0.7709 (pm20) REVERT: B 387 MET cc_start: 0.7990 (mtm) cc_final: 0.7682 (mtm) REVERT: B 400 GLU cc_start: 0.7933 (tt0) cc_final: 0.7546 (tt0) REVERT: B 402 LYS cc_start: 0.6772 (mtpt) cc_final: 0.6169 (mptt) REVERT: B 426 ILE cc_start: 0.9085 (mt) cc_final: 0.8833 (mm) REVERT: B 428 GLN cc_start: 0.8446 (mt0) cc_final: 0.8242 (mt0) REVERT: C 3 GLN cc_start: 0.7627 (tt0) cc_final: 0.7057 (mm-40) REVERT: C 32 TYR cc_start: 0.7811 (m-80) cc_final: 0.7391 (m-80) REVERT: C 100 ASP cc_start: 0.8450 (p0) cc_final: 0.8171 (p0) REVERT: C 122 LYS cc_start: 0.7556 (tttt) cc_final: 0.7218 (tttm) REVERT: D 70 ASP cc_start: 0.8047 (t70) cc_final: 0.7825 (t70) REVERT: D 103 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7978 (ttpp) REVERT: D 105 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7111 (mt-10) outliers start: 34 outliers final: 10 residues processed: 209 average time/residue: 1.1499 time to fit residues: 258.3912 Evaluate side-chains 159 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 134 GLN A 451 GLN B 267 GLN B 274 HIS B 280 HIS C 3 GLN D 124 GLN D 137 ASN D 147 GLN D 155 GLN D 166 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.092314 restraints weight = 9679.269| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.48 r_work: 0.2717 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9948 Z= 0.186 Angle : 0.586 8.539 13534 Z= 0.312 Chirality : 0.046 0.152 1496 Planarity : 0.004 0.040 1758 Dihedral : 7.503 58.332 1396 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.81 % Allowed : 12.00 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1254 helix: -1.83 (0.40), residues: 121 sheet: -0.94 (0.23), residues: 448 loop : -1.17 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 33 HIS 0.005 0.001 HIS A 278 PHE 0.014 0.002 PHE A 19 TYR 0.013 0.002 TYR D 50 ARG 0.007 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 329) hydrogen bonds : angle 6.94769 ( 888) SS BOND : bond 0.00762 ( 10) SS BOND : angle 1.64506 ( 20) covalent geometry : bond 0.00426 ( 9938) covalent geometry : angle 0.58315 (13514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.935 Fit side-chains REVERT: A 76 THR cc_start: 0.9024 (t) cc_final: 0.8822 (m) REVERT: A 77 ARG cc_start: 0.7605 (mpt180) cc_final: 0.6910 (ttt-90) REVERT: A 120 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 125 THR cc_start: 0.8957 (p) cc_final: 0.8501 (p) REVERT: A 166 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: A 197 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8447 (pp30) REVERT: A 208 ARG cc_start: 0.8456 (mpt180) cc_final: 0.8149 (mmt-90) REVERT: A 355 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8823 (mtt180) REVERT: A 400 ARG cc_start: 0.8271 (mmt180) cc_final: 0.7672 (mmt90) REVERT: A 401 SER cc_start: 0.8876 (p) cc_final: 0.8634 (m) REVERT: B 93 ARG cc_start: 0.7415 (ptm160) cc_final: 0.6473 (ttt180) REVERT: B 108 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 137 LYS cc_start: 0.8554 (mttt) cc_final: 0.8087 (mtmt) REVERT: B 187 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8137 (tmm) REVERT: B 277 SER cc_start: 0.8975 (p) cc_final: 0.8668 (m) REVERT: B 323 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8113 (mt-10) REVERT: B 365 GLU cc_start: 0.8336 (mp0) cc_final: 0.8065 (pm20) REVERT: B 387 MET cc_start: 0.8771 (mtm) cc_final: 0.8312 (mtm) REVERT: B 400 GLU cc_start: 0.8322 (tt0) cc_final: 0.8022 (tt0) REVERT: B 402 LYS cc_start: 0.7298 (mtpt) cc_final: 0.6799 (mptt) REVERT: C 3 GLN cc_start: 0.7826 (tt0) cc_final: 0.7305 (mm-40) REVERT: C 32 TYR cc_start: 0.8183 (m-80) cc_final: 0.7837 (m-80) REVERT: C 69 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8285 (tttt) REVERT: C 122 LYS cc_start: 0.7639 (tttt) cc_final: 0.7261 (tttm) REVERT: D 55 MET cc_start: 0.8834 (mmm) cc_final: 0.8466 (mmm) REVERT: D 79 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: D 81 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: D 175 LEU cc_start: 0.7441 (tt) cc_final: 0.7200 (tt) outliers start: 41 outliers final: 21 residues processed: 180 average time/residue: 1.6412 time to fit residues: 318.8100 Evaluate side-chains 167 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 90 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.147752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.103378 restraints weight = 9798.600| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.27 r_work: 0.2716 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9948 Z= 0.166 Angle : 0.550 7.388 13534 Z= 0.291 Chirality : 0.045 0.146 1496 Planarity : 0.004 0.040 1758 Dihedral : 7.097 59.859 1390 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 4.28 % Allowed : 13.30 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1254 helix: -1.22 (0.43), residues: 122 sheet: -0.63 (0.24), residues: 446 loop : -0.87 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 33 HIS 0.005 0.001 HIS A 215 PHE 0.014 0.002 PHE A 19 TYR 0.023 0.002 TYR C 150 ARG 0.008 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 329) hydrogen bonds : angle 6.45443 ( 888) SS BOND : bond 0.00520 ( 10) SS BOND : angle 1.55357 ( 20) covalent geometry : bond 0.00378 ( 9938) covalent geometry : angle 0.54680 (13514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.870 Fit side-chains REVERT: A 77 ARG cc_start: 0.7729 (mpt180) cc_final: 0.6801 (ttt-90) REVERT: A 120 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 125 THR cc_start: 0.9027 (p) cc_final: 0.8607 (p) REVERT: A 166 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: A 355 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8787 (mtt180) REVERT: A 401 SER cc_start: 0.8886 (p) cc_final: 0.8665 (m) REVERT: B 93 ARG cc_start: 0.7299 (ptm160) cc_final: 0.6242 (ttt180) REVERT: B 108 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7920 (mt-10) REVERT: B 137 LYS cc_start: 0.8566 (mttt) cc_final: 0.8094 (mtmt) REVERT: B 187 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8193 (tmm) REVERT: B 277 SER cc_start: 0.9012 (p) cc_final: 0.8678 (m) REVERT: B 278 ASP cc_start: 0.8292 (p0) cc_final: 0.8079 (p0) REVERT: B 312 GLU cc_start: 0.8097 (tp30) cc_final: 0.7868 (mm-30) REVERT: B 323 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8094 (mt-10) REVERT: B 365 GLU cc_start: 0.8343 (mp0) cc_final: 0.8063 (pm20) REVERT: B 387 MET cc_start: 0.8828 (mtm) cc_final: 0.8331 (mtm) REVERT: B 400 GLU cc_start: 0.8388 (tt0) cc_final: 0.7967 (tt0) REVERT: B 402 LYS cc_start: 0.7016 (mtpt) cc_final: 0.6784 (tptp) REVERT: B 422 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8399 (pttp) REVERT: C 3 GLN cc_start: 0.7854 (tt0) cc_final: 0.7338 (mm-40) REVERT: C 19 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8987 (ttpp) REVERT: C 32 TYR cc_start: 0.8203 (m-80) cc_final: 0.7871 (m-80) REVERT: C 122 LYS cc_start: 0.7557 (tttt) cc_final: 0.7275 (tttp) REVERT: D 81 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: D 103 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8113 (ttpp) outliers start: 46 outliers final: 21 residues processed: 176 average time/residue: 1.4311 time to fit residues: 269.7652 Evaluate side-chains 168 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 39 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.149229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.104070 restraints weight = 9641.058| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.01 r_work: 0.2716 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9948 Z= 0.161 Angle : 0.542 8.458 13534 Z= 0.286 Chirality : 0.045 0.143 1496 Planarity : 0.004 0.037 1758 Dihedral : 6.837 58.395 1389 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 4.09 % Allowed : 14.51 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1254 helix: -0.85 (0.45), residues: 122 sheet: -0.49 (0.24), residues: 456 loop : -0.70 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 33 HIS 0.005 0.001 HIS A 215 PHE 0.014 0.002 PHE A 19 TYR 0.013 0.001 TYR D 50 ARG 0.008 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 329) hydrogen bonds : angle 6.22780 ( 888) SS BOND : bond 0.00599 ( 10) SS BOND : angle 1.45200 ( 20) covalent geometry : bond 0.00367 ( 9938) covalent geometry : angle 0.53981 (13514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 1.125 Fit side-chains REVERT: A 77 ARG cc_start: 0.7681 (mpt180) cc_final: 0.6953 (ttt-90) REVERT: A 125 THR cc_start: 0.8915 (p) cc_final: 0.8474 (p) REVERT: A 166 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: A 192 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 386 ARG cc_start: 0.8678 (mtm110) cc_final: 0.8422 (mtp180) REVERT: A 401 SER cc_start: 0.8885 (p) cc_final: 0.8662 (m) REVERT: B 93 ARG cc_start: 0.7294 (ptm160) cc_final: 0.6230 (ttt180) REVERT: B 137 LYS cc_start: 0.8561 (mttt) cc_final: 0.8100 (mtmt) REVERT: B 187 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8154 (tmm) REVERT: B 234 GLU cc_start: 0.7764 (pm20) cc_final: 0.7429 (pm20) REVERT: B 277 SER cc_start: 0.9012 (p) cc_final: 0.8661 (m) REVERT: B 278 ASP cc_start: 0.8319 (p0) cc_final: 0.8082 (p0) REVERT: B 312 GLU cc_start: 0.8085 (tp30) cc_final: 0.7883 (mm-30) REVERT: B 323 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8091 (mt-10) REVERT: B 365 GLU cc_start: 0.8320 (mp0) cc_final: 0.8029 (pm20) REVERT: B 387 MET cc_start: 0.8831 (mtm) cc_final: 0.8286 (mtm) REVERT: B 400 GLU cc_start: 0.8264 (tt0) cc_final: 0.7870 (tt0) REVERT: B 402 LYS cc_start: 0.7002 (mtpt) cc_final: 0.6769 (tptp) REVERT: B 422 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8421 (pttp) REVERT: C 3 GLN cc_start: 0.7844 (tt0) cc_final: 0.7343 (mm-40) REVERT: C 32 TYR cc_start: 0.8208 (m-80) cc_final: 0.7885 (m-80) REVERT: C 67 LYS cc_start: 0.8485 (tppt) cc_final: 0.8264 (tppt) REVERT: C 122 LYS cc_start: 0.7558 (tttt) cc_final: 0.7329 (tttp) REVERT: D 55 MET cc_start: 0.8844 (mmm) cc_final: 0.8537 (mmm) REVERT: D 81 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: D 103 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8066 (ttpp) outliers start: 44 outliers final: 21 residues processed: 179 average time/residue: 1.2359 time to fit residues: 237.1588 Evaluate side-chains 169 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.150577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.106340 restraints weight = 9703.717| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.04 r_work: 0.2757 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9948 Z= 0.118 Angle : 0.505 8.384 13534 Z= 0.266 Chirality : 0.044 0.144 1496 Planarity : 0.004 0.039 1758 Dihedral : 6.559 59.348 1388 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 3.91 % Allowed : 15.44 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1254 helix: -0.48 (0.46), residues: 122 sheet: -0.27 (0.24), residues: 447 loop : -0.57 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 235 HIS 0.005 0.001 HIS A 215 PHE 0.012 0.001 PHE A 191 TYR 0.028 0.001 TYR C 150 ARG 0.008 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 329) hydrogen bonds : angle 5.90858 ( 888) SS BOND : bond 0.00580 ( 10) SS BOND : angle 1.26296 ( 20) covalent geometry : bond 0.00267 ( 9938) covalent geometry : angle 0.50258 (13514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7547 (mpt180) cc_final: 0.6693 (ttt-90) REVERT: A 125 THR cc_start: 0.9035 (p) cc_final: 0.8797 (p) REVERT: A 153 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8249 (ptt90) REVERT: B 62 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7681 (mtm110) REVERT: B 72 LYS cc_start: 0.8130 (ptmm) cc_final: 0.7885 (ptmm) REVERT: B 93 ARG cc_start: 0.7258 (ptm160) cc_final: 0.6176 (ttt180) REVERT: B 137 LYS cc_start: 0.8486 (mttt) cc_final: 0.8020 (mtmt) REVERT: B 187 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8181 (tmm) REVERT: B 234 GLU cc_start: 0.7804 (pm20) cc_final: 0.7368 (pm20) REVERT: B 277 SER cc_start: 0.8990 (p) cc_final: 0.8664 (m) REVERT: B 323 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8069 (mt-10) REVERT: B 365 GLU cc_start: 0.8283 (mp0) cc_final: 0.8029 (pm20) REVERT: B 387 MET cc_start: 0.8808 (mtm) cc_final: 0.8278 (mtm) REVERT: B 400 GLU cc_start: 0.8251 (tt0) cc_final: 0.7858 (tt0) REVERT: C 3 GLN cc_start: 0.7855 (tt0) cc_final: 0.7380 (mm-40) REVERT: C 32 TYR cc_start: 0.8175 (m-80) cc_final: 0.7836 (m-80) REVERT: C 63 LYS cc_start: 0.8322 (tttm) cc_final: 0.8098 (tttt) REVERT: D 38 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: D 55 MET cc_start: 0.8789 (mmm) cc_final: 0.8365 (mmm) REVERT: D 103 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8053 (ttpp) outliers start: 42 outliers final: 21 residues processed: 184 average time/residue: 1.2117 time to fit residues: 239.4300 Evaluate side-chains 165 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 124 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.151071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.105837 restraints weight = 9728.016| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.78 r_work: 0.2754 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9948 Z= 0.117 Angle : 0.502 9.038 13534 Z= 0.264 Chirality : 0.043 0.142 1496 Planarity : 0.004 0.037 1758 Dihedral : 6.274 58.420 1385 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 4.19 % Allowed : 16.19 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1254 helix: -0.26 (0.48), residues: 117 sheet: -0.19 (0.24), residues: 445 loop : -0.49 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 33 HIS 0.005 0.001 HIS A 215 PHE 0.011 0.001 PHE A 191 TYR 0.011 0.001 TYR D 50 ARG 0.009 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 329) hydrogen bonds : angle 5.80955 ( 888) SS BOND : bond 0.00552 ( 10) SS BOND : angle 1.29053 ( 20) covalent geometry : bond 0.00265 ( 9938) covalent geometry : angle 0.49969 (13514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.125 Fit side-chains REVERT: A 77 ARG cc_start: 0.7552 (mpt180) cc_final: 0.6753 (ttt-90) REVERT: A 125 THR cc_start: 0.9034 (p) cc_final: 0.8799 (p) REVERT: A 192 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 355 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8738 (mtt90) REVERT: A 386 ARG cc_start: 0.8661 (mtm110) cc_final: 0.8459 (mtp-110) REVERT: A 400 ARG cc_start: 0.8404 (mmt180) cc_final: 0.7829 (mmt90) REVERT: B 62 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7603 (mtm110) REVERT: B 72 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7870 (tptt) REVERT: B 93 ARG cc_start: 0.7337 (ptm160) cc_final: 0.6141 (ttt180) REVERT: B 137 LYS cc_start: 0.8524 (mttt) cc_final: 0.8061 (mtmt) REVERT: B 187 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8154 (tmm) REVERT: B 234 GLU cc_start: 0.7819 (pm20) cc_final: 0.7396 (pm20) REVERT: B 277 SER cc_start: 0.8971 (p) cc_final: 0.8649 (m) REVERT: B 323 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8079 (mt-10) REVERT: B 365 GLU cc_start: 0.8286 (mp0) cc_final: 0.8061 (pm20) REVERT: B 387 MET cc_start: 0.8793 (mtm) cc_final: 0.8267 (mtm) REVERT: B 400 GLU cc_start: 0.8136 (tt0) cc_final: 0.7786 (tt0) REVERT: B 402 LYS cc_start: 0.7839 (tptp) cc_final: 0.7365 (tppt) REVERT: C 3 GLN cc_start: 0.7814 (tt0) cc_final: 0.7372 (mm-40) REVERT: C 32 TYR cc_start: 0.8142 (m-80) cc_final: 0.7764 (m-80) REVERT: C 63 LYS cc_start: 0.8280 (tttm) cc_final: 0.8048 (tttt) REVERT: C 69 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8135 (tttt) REVERT: D 55 MET cc_start: 0.8793 (mmm) cc_final: 0.8416 (mmm) REVERT: D 103 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8032 (ttpp) outliers start: 45 outliers final: 25 residues processed: 185 average time/residue: 1.4180 time to fit residues: 280.2392 Evaluate side-chains 174 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.147849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.103606 restraints weight = 9754.457| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.35 r_work: 0.2713 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9948 Z= 0.196 Angle : 0.554 11.207 13534 Z= 0.290 Chirality : 0.045 0.146 1496 Planarity : 0.004 0.040 1758 Dihedral : 6.491 59.027 1385 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.19 % Allowed : 16.09 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1254 helix: -0.45 (0.46), residues: 122 sheet: -0.28 (0.24), residues: 452 loop : -0.46 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 33 HIS 0.005 0.001 HIS A 215 PHE 0.016 0.002 PHE A 19 TYR 0.015 0.002 TYR D 50 ARG 0.009 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 329) hydrogen bonds : angle 5.98356 ( 888) SS BOND : bond 0.00685 ( 10) SS BOND : angle 1.57797 ( 20) covalent geometry : bond 0.00451 ( 9938) covalent geometry : angle 0.55109 (13514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 2.265 Fit side-chains REVERT: A 77 ARG cc_start: 0.7703 (mpt180) cc_final: 0.6847 (ttt-90) REVERT: A 125 THR cc_start: 0.9002 (p) cc_final: 0.8659 (p) REVERT: A 192 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 386 ARG cc_start: 0.8672 (mtm110) cc_final: 0.8395 (mtp180) REVERT: B 72 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7896 (tptt) REVERT: B 93 ARG cc_start: 0.7297 (ptm160) cc_final: 0.6104 (ttt180) REVERT: B 137 LYS cc_start: 0.8569 (mttt) cc_final: 0.8116 (mtmt) REVERT: B 187 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8073 (tmm) REVERT: B 234 GLU cc_start: 0.7801 (pm20) cc_final: 0.7369 (pm20) REVERT: B 277 SER cc_start: 0.8994 (p) cc_final: 0.8657 (m) REVERT: B 323 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8156 (mt-10) REVERT: B 360 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8052 (mmt90) REVERT: B 365 GLU cc_start: 0.8269 (mp0) cc_final: 0.7970 (pm20) REVERT: B 387 MET cc_start: 0.8794 (mtm) cc_final: 0.8233 (mtm) REVERT: B 400 GLU cc_start: 0.8140 (tt0) cc_final: 0.7725 (tt0) REVERT: C 3 GLN cc_start: 0.7824 (tt0) cc_final: 0.7380 (mm-40) REVERT: C 32 TYR cc_start: 0.8183 (m-80) cc_final: 0.7817 (m-80) REVERT: C 69 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8139 (tttt) REVERT: D 79 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7589 (mm-30) REVERT: D 103 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8136 (ttpp) outliers start: 45 outliers final: 28 residues processed: 179 average time/residue: 1.3656 time to fit residues: 264.4799 Evaluate side-chains 178 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 109 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.148904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.093679 restraints weight = 9818.081| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.50 r_work: 0.2738 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9948 Z= 0.154 Angle : 0.531 10.858 13534 Z= 0.278 Chirality : 0.044 0.141 1496 Planarity : 0.004 0.039 1758 Dihedral : 6.422 59.050 1385 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.44 % Allowed : 17.21 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1254 helix: -0.30 (0.47), residues: 122 sheet: -0.23 (0.24), residues: 452 loop : -0.41 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 33 HIS 0.007 0.001 HIS A 215 PHE 0.013 0.002 PHE A 19 TYR 0.013 0.001 TYR D 50 ARG 0.009 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 329) hydrogen bonds : angle 5.89666 ( 888) SS BOND : bond 0.00553 ( 10) SS BOND : angle 1.44262 ( 20) covalent geometry : bond 0.00353 ( 9938) covalent geometry : angle 0.52871 (13514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7604 (mpt180) cc_final: 0.6803 (ttt-90) REVERT: A 125 THR cc_start: 0.8916 (p) cc_final: 0.8571 (p) REVERT: A 192 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 386 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8308 (mtp180) REVERT: A 400 ARG cc_start: 0.8382 (mmt180) cc_final: 0.7795 (mmt90) REVERT: B 72 LYS cc_start: 0.8133 (ptmm) cc_final: 0.7919 (tptt) REVERT: B 93 ARG cc_start: 0.7333 (ptm160) cc_final: 0.6095 (ttt180) REVERT: B 137 LYS cc_start: 0.8542 (mttt) cc_final: 0.8100 (mtmt) REVERT: B 234 GLU cc_start: 0.7769 (pm20) cc_final: 0.7285 (pm20) REVERT: B 277 SER cc_start: 0.8987 (p) cc_final: 0.8656 (m) REVERT: B 323 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8095 (mt-10) REVERT: B 365 GLU cc_start: 0.8266 (mp0) cc_final: 0.7990 (pm20) REVERT: B 387 MET cc_start: 0.8788 (mtm) cc_final: 0.8232 (mtm) REVERT: B 400 GLU cc_start: 0.8201 (tt0) cc_final: 0.7779 (tt0) REVERT: C 3 GLN cc_start: 0.7831 (tt0) cc_final: 0.7392 (mm-40) REVERT: C 32 TYR cc_start: 0.8138 (m-80) cc_final: 0.7772 (m-80) REVERT: D 55 MET cc_start: 0.8737 (mmm) cc_final: 0.8348 (mmm) REVERT: D 79 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: D 103 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8087 (ttpp) REVERT: D 205 VAL cc_start: 0.6082 (OUTLIER) cc_final: 0.5740 (p) outliers start: 37 outliers final: 26 residues processed: 170 average time/residue: 1.2860 time to fit residues: 234.6037 Evaluate side-chains 173 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.148818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.104885 restraints weight = 9756.000| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.12 r_work: 0.2723 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9948 Z= 0.174 Angle : 0.547 11.742 13534 Z= 0.286 Chirality : 0.045 0.145 1496 Planarity : 0.004 0.040 1758 Dihedral : 6.287 58.672 1382 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 17.30 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1254 helix: -0.32 (0.46), residues: 122 sheet: -0.25 (0.24), residues: 453 loop : -0.40 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 33 HIS 0.007 0.001 HIS A 215 PHE 0.015 0.002 PHE A 19 TYR 0.014 0.002 TYR D 50 ARG 0.009 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 329) hydrogen bonds : angle 5.92317 ( 888) SS BOND : bond 0.00656 ( 10) SS BOND : angle 1.53716 ( 20) covalent geometry : bond 0.00399 ( 9938) covalent geometry : angle 0.54390 (13514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.056 Fit side-chains REVERT: A 75 GLU cc_start: 0.8547 (mp0) cc_final: 0.8245 (mt-10) REVERT: A 77 ARG cc_start: 0.7687 (mpt180) cc_final: 0.6811 (ttt-90) REVERT: A 125 THR cc_start: 0.8960 (p) cc_final: 0.8616 (p) REVERT: A 192 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8465 (mp) REVERT: A 386 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8256 (mtp180) REVERT: B 60 GLU cc_start: 0.7747 (pt0) cc_final: 0.7418 (pm20) REVERT: B 72 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7796 (tptt) REVERT: B 93 ARG cc_start: 0.7385 (ptm160) cc_final: 0.6077 (ttt180) REVERT: B 108 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 137 LYS cc_start: 0.8534 (mttt) cc_final: 0.8091 (mtmt) REVERT: B 234 GLU cc_start: 0.7781 (pm20) cc_final: 0.7210 (mp0) REVERT: B 277 SER cc_start: 0.8989 (p) cc_final: 0.8656 (m) REVERT: B 323 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8124 (mt-10) REVERT: B 365 GLU cc_start: 0.8244 (mp0) cc_final: 0.7932 (pm20) REVERT: B 387 MET cc_start: 0.8767 (mtm) cc_final: 0.8196 (mtm) REVERT: B 400 GLU cc_start: 0.8203 (tt0) cc_final: 0.7791 (tt0) REVERT: C 3 GLN cc_start: 0.7826 (tt0) cc_final: 0.7364 (mm-40) REVERT: C 32 TYR cc_start: 0.8161 (m-80) cc_final: 0.7777 (m-80) REVERT: D 55 MET cc_start: 0.8755 (mmm) cc_final: 0.8343 (mmm) REVERT: D 79 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: D 103 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8104 (ttpp) REVERT: D 205 VAL cc_start: 0.6063 (OUTLIER) cc_final: 0.5731 (p) outliers start: 36 outliers final: 28 residues processed: 166 average time/residue: 1.2590 time to fit residues: 224.3080 Evaluate side-chains 173 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 32 ASN D 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.150171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.099720 restraints weight = 9828.532| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.37 r_work: 0.2753 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9948 Z= 0.133 Angle : 0.517 10.445 13534 Z= 0.271 Chirality : 0.044 0.141 1496 Planarity : 0.004 0.041 1758 Dihedral : 6.175 58.757 1382 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.26 % Allowed : 17.49 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1254 helix: -0.22 (0.47), residues: 122 sheet: -0.15 (0.24), residues: 453 loop : -0.37 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 33 HIS 0.007 0.001 HIS A 215 PHE 0.013 0.001 PHE A 131 TYR 0.012 0.001 TYR D 50 ARG 0.010 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 329) hydrogen bonds : angle 5.78630 ( 888) SS BOND : bond 0.00616 ( 10) SS BOND : angle 1.35482 ( 20) covalent geometry : bond 0.00305 ( 9938) covalent geometry : angle 0.51522 (13514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8548 (mp0) cc_final: 0.8258 (mt-10) REVERT: A 77 ARG cc_start: 0.7585 (mpt180) cc_final: 0.6769 (ttt-90) REVERT: A 125 THR cc_start: 0.8963 (p) cc_final: 0.8666 (p) REVERT: A 192 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 368 ARG cc_start: 0.8670 (mtm180) cc_final: 0.8454 (mtp-110) REVERT: A 386 ARG cc_start: 0.8554 (mtm110) cc_final: 0.8289 (mtp180) REVERT: A 400 ARG cc_start: 0.8367 (mmt180) cc_final: 0.7782 (mmt90) REVERT: B 93 ARG cc_start: 0.7346 (ptm160) cc_final: 0.6055 (ttt180) REVERT: B 137 LYS cc_start: 0.8532 (mttt) cc_final: 0.8104 (mtmt) REVERT: B 234 GLU cc_start: 0.7788 (pm20) cc_final: 0.7237 (mp0) REVERT: B 277 SER cc_start: 0.8947 (p) cc_final: 0.8624 (m) REVERT: B 323 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8094 (mt-10) REVERT: B 365 GLU cc_start: 0.8243 (mp0) cc_final: 0.7947 (pm20) REVERT: B 387 MET cc_start: 0.8767 (mtm) cc_final: 0.8209 (mtm) REVERT: B 400 GLU cc_start: 0.8149 (tt0) cc_final: 0.7755 (tt0) REVERT: B 402 LYS cc_start: 0.7784 (tptp) cc_final: 0.7388 (tppt) REVERT: C 3 GLN cc_start: 0.7808 (tt0) cc_final: 0.7367 (mm-40) REVERT: C 32 TYR cc_start: 0.8158 (m-80) cc_final: 0.7772 (m-80) REVERT: C 81 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8043 (ttm) REVERT: D 55 MET cc_start: 0.8773 (mmm) cc_final: 0.8426 (mmm) REVERT: D 103 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8034 (ttpp) REVERT: D 105 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7437 (mp0) REVERT: D 205 VAL cc_start: 0.6074 (OUTLIER) cc_final: 0.5751 (p) outliers start: 35 outliers final: 24 residues processed: 166 average time/residue: 1.5991 time to fit residues: 285.3473 Evaluate side-chains 166 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5414 > 50: distance: 102 - 179: 4.593 distance: 105 - 176: 5.240 distance: 109 - 117: 4.721 distance: 117 - 118: 7.337 distance: 118 - 119: 9.823 distance: 118 - 121: 12.256 distance: 119 - 120: 25.058 distance: 119 - 125: 17.561 distance: 121 - 122: 6.942 distance: 122 - 123: 4.376 distance: 122 - 124: 4.282 distance: 125 - 126: 19.730 distance: 126 - 127: 16.837 distance: 127 - 128: 36.151 distance: 127 - 129: 20.948 distance: 129 - 130: 15.859 distance: 130 - 131: 6.109 distance: 130 - 133: 6.770 distance: 131 - 132: 6.586 distance: 133 - 134: 5.193 distance: 134 - 135: 3.330 distance: 134 - 136: 5.164 distance: 136 - 138: 3.819 distance: 138 - 139: 3.574 distance: 139 - 140: 5.590 distance: 141 - 142: 3.187 distance: 143 - 144: 3.342 distance: 145 - 146: 3.991 distance: 146 - 147: 3.017 distance: 150 - 151: 3.208 distance: 151 - 152: 7.331 distance: 154 - 155: 7.252 distance: 155 - 160: 5.445 distance: 157 - 159: 7.513 distance: 160 - 161: 5.885 distance: 161 - 162: 4.845 distance: 161 - 164: 3.337 distance: 162 - 163: 4.868 distance: 162 - 171: 4.464 distance: 164 - 165: 3.628 distance: 165 - 166: 4.346 distance: 165 - 167: 3.339 distance: 166 - 168: 7.251 distance: 167 - 169: 3.047 distance: 168 - 170: 5.705 distance: 169 - 170: 4.124 distance: 172 - 175: 5.751 distance: 173 - 174: 9.433 distance: 176 - 177: 10.664 distance: 177 - 178: 8.988 distance: 177 - 180: 10.867 distance: 178 - 179: 4.616 distance: 178 - 188: 3.669 distance: 180 - 181: 5.698 distance: 181 - 182: 5.762 distance: 182 - 184: 3.008 distance: 184 - 186: 4.315 distance: 186 - 187: 5.788 distance: 189 - 190: 5.081 distance: 189 - 192: 3.553 distance: 190 - 191: 4.155 distance: 190 - 202: 11.387 distance: 194 - 196: 3.640 distance: 202 - 203: 18.970 distance: 203 - 204: 13.005 distance: 204 - 205: 9.859 distance: 204 - 206: 3.541