Starting phenix.real_space_refine on Tue Mar 3 13:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xi8_22191/03_2026/6xi8_22191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xi8_22191/03_2026/6xi8_22191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xi8_22191/03_2026/6xi8_22191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xi8_22191/03_2026/6xi8_22191.map" model { file = "/net/cci-nas-00/data/ceres_data/6xi8_22191/03_2026/6xi8_22191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xi8_22191/03_2026/6xi8_22191.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 S 24 5.16 5 C 3229 2.51 5 N 836 2.21 5 O 926 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5022 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 499 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2342 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 3, 'GLU:plan': 10, 'ASN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.29, per 1000 atoms: 0.26 Number of scatterers: 5022 At special positions: 0 Unit cell: (96.28, 85.49, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 24 16.00 P 3 15.00 Al 1 13.00 F 3 9.00 O 926 8.00 N 836 7.00 C 3229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.42 Conformation dependent library (CDL) restraints added in 319.4 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 51.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'C' and resid 284 through 287 removed outlier: 3.524A pdb=" N HIS C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.092A pdb=" N ILE C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.787A pdb=" N ALA C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 removed outlier: 3.988A pdb=" N ILE A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 3.774A pdb=" N VAL A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 123 removed outlier: 3.548A pdb=" N ALA A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TRP A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.770A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 185 through 201 removed outlier: 3.915A pdb=" N TRP A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 4.106A pdb=" N GLU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.507A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 252' Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.731A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.771A pdb=" N MET B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 94 through 106 Processing helix chain 'B' and resid 108 through 131 removed outlier: 5.504A pdb=" N LEU B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 4.109A pdb=" N GLU B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.973A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N HIS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 223 through 229 removed outlier: 3.594A pdb=" N VAL B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 271 Processing helix chain 'B' and resid 272 through 275 removed outlier: 3.618A pdb=" N ASP B 275 " --> pdb=" O LEU B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.932A pdb=" N THR B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 345 removed outlier: 4.070A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 360 removed outlier: 4.124A pdb=" N LYS B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.884A pdb=" N VAL A 20 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 79 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 136 167 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 823 1.31 - 1.44: 1360 1.44 - 1.56: 2900 1.56 - 1.69: 10 1.69 - 1.81: 43 Bond restraints: 5136 Sorted by residual: bond pdb=" C THR B 351 " pdb=" N GLU B 352 " ideal model delta sigma weight residual 1.333 1.554 -0.222 1.45e-02 4.76e+03 2.34e+02 bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.301 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 1.426 1.629 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.27e-02 6.20e+03 8.97e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 5131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.35: 6922 7.35 - 14.69: 42 14.69 - 22.04: 3 22.04 - 29.38: 3 29.38 - 36.73: 4 Bond angle restraints: 6974 Sorted by residual: angle pdb=" O GLU B 344 " pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 122.43 85.70 36.73 1.46e+00 4.69e-01 6.33e+02 angle pdb=" N ASP A 228 " pdb=" CA ASP A 228 " pdb=" C ASP A 228 " ideal model delta sigma weight residual 112.04 143.07 -31.03 1.44e+00 4.82e-01 4.64e+02 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 111.92 128.88 -16.96 1.34e+00 5.57e-01 1.60e+02 angle pdb=" C ASP A 228 " pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " ideal model delta sigma weight residual 110.56 88.32 22.24 1.83e+00 2.99e-01 1.48e+02 angle pdb=" O2P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 113.68 78.53 35.15 3.00e+00 1.11e-01 1.37e+02 ... (remaining 6969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 3010 32.62 - 65.23: 76 65.23 - 97.85: 4 97.85 - 130.47: 0 130.47 - 163.08: 1 Dihedral angle restraints: 3091 sinusoidal: 1201 harmonic: 1890 Sorted by residual: dihedral pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual 122.80 167.25 -44.45 0 2.50e+00 1.60e-01 3.16e+02 dihedral pdb=" C PHE B 177 " pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual -122.60 -166.09 43.49 0 2.50e+00 1.60e-01 3.03e+02 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.92 163.08 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 3088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 785 0.402 - 0.803: 4 0.803 - 1.205: 0 1.205 - 1.607: 0 1.607 - 2.008: 1 Chirality restraints: 790 Sorted by residual: chirality pdb=" CA PHE B 177 " pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CB PHE B 177 " both_signs ideal model delta sigma weight residual False 2.51 0.50 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA ASP A 228 " pdb=" N ASP A 228 " pdb=" C ASP A 228 " pdb=" CB ASP A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA TYR B 362 " pdb=" N TYR B 362 " pdb=" C TYR B 362 " pdb=" CB TYR B 362 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 787 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 344 " -0.123 2.00e-02 2.50e+03 1.90e-01 3.61e+02 pdb=" C GLU B 344 " 0.328 2.00e-02 2.50e+03 pdb=" O GLU B 344 " -0.112 2.00e-02 2.50e+03 pdb=" N ASP B 345 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.061 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C THR B 351 " 0.183 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.069 2.00e-02 2.50e+03 pdb=" N GLU B 352 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " -0.039 2.00e-02 2.50e+03 4.06e-02 4.13e+01 pdb=" CG TRP B 58 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP B 58 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 58 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 58 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 58 " -0.003 2.00e-02 2.50e+03 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 1 2.05 - 2.76: 684 2.76 - 3.47: 6721 3.47 - 4.19: 11340 4.19 - 4.90: 19672 Nonbonded interactions: 38418 Sorted by model distance: nonbonded pdb=" O CYS B 364 " pdb=" CG PRO B 367 " model vdw 1.333 3.440 nonbonded pdb=" C CYS B 364 " pdb=" CG PRO B 367 " model vdw 2.113 3.670 nonbonded pdb=" O CYS B 364 " pdb=" CD PRO B 367 " model vdw 2.160 3.440 nonbonded pdb=" CG PRO A 224 " pdb=" SD MET A 273 " model vdw 2.205 3.800 nonbonded pdb=" O GLU B 344 " pdb=" N CYS B 346 " model vdw 2.215 3.120 ... (remaining 38413 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=0.77 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 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 : 0.010 0.223 5136 Z= 0.558 Angle : 1.686 36.730 6974 Z= 0.897 Chirality : 0.111 2.008 790 Planarity : 0.012 0.190 881 Dihedral : 15.204 163.082 1859 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.77 % Allowed : 1.35 % Favored : 97.88 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.27), residues: 621 helix: -3.24 (0.21), residues: 289 sheet: -3.17 (0.77), residues: 35 loop : -2.79 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 50 TYR 0.056 0.003 TYR A 57 PHE 0.028 0.003 PHE B 177 TRP 0.105 0.006 TRP B 58 HIS 0.008 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.01020 ( 5136) covalent geometry : angle 1.68579 ( 6974) hydrogen bonds : bond 0.18038 ( 167) hydrogen bonds : angle 7.41001 ( 489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7274 (m-80) cc_final: 0.6975 (m-80) REVERT: A 47 LEU cc_start: 0.7122 (mp) cc_final: 0.6829 (mp) REVERT: A 56 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6934 (pttt) REVERT: A 266 PHE cc_start: 0.7277 (p90) cc_final: 0.6102 (p90) REVERT: B 122 LYS cc_start: 0.7716 (tptt) cc_final: 0.7086 (tptp) REVERT: B 145 PHE cc_start: 0.6492 (t80) cc_final: 0.5936 (t80) REVERT: B 173 SER cc_start: 0.8682 (t) cc_final: 0.8273 (t) REVERT: B 221 PHE cc_start: 0.6836 (m-10) cc_final: 0.6629 (m-80) REVERT: B 261 TYR cc_start: 0.5351 (m-80) cc_final: 0.5020 (m-80) REVERT: B 280 THR cc_start: 0.7529 (m) cc_final: 0.6935 (m) outliers start: 4 outliers final: 0 residues processed: 185 average time/residue: 0.0867 time to fit residues: 19.7315 Evaluate side-chains 168 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN B 212 HIS B 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.158582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.135101 restraints weight = 10200.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.139143 restraints weight = 6285.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.141873 restraints weight = 4363.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143868 restraints weight = 3299.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.145338 restraints weight = 2648.563| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4189 r_free = 0.4189 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5136 Z= 0.152 Angle : 0.795 10.191 6974 Z= 0.399 Chirality : 0.050 0.257 790 Planarity : 0.008 0.069 881 Dihedral : 8.849 161.716 697 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.93 % Allowed : 13.90 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.30), residues: 621 helix: -1.91 (0.26), residues: 287 sheet: -2.81 (0.84), residues: 33 loop : -2.26 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 244 TYR 0.022 0.002 TYR B 261 PHE 0.019 0.002 PHE A 266 TRP 0.024 0.002 TRP B 58 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5136) covalent geometry : angle 0.79514 ( 6974) hydrogen bonds : bond 0.04287 ( 167) hydrogen bonds : angle 5.04955 ( 489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 ARG cc_start: 0.6755 (mtm180) cc_final: 0.6554 (mtm110) REVERT: A 266 PHE cc_start: 0.7926 (p90) cc_final: 0.7355 (p90) REVERT: B 66 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7208 (tp-100) REVERT: B 122 LYS cc_start: 0.8215 (tptt) cc_final: 0.7587 (tptp) REVERT: B 125 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 145 PHE cc_start: 0.7537 (t80) cc_final: 0.6971 (t80) REVERT: B 169 LEU cc_start: 0.7288 (tp) cc_final: 0.6801 (tp) REVERT: B 173 SER cc_start: 0.8241 (t) cc_final: 0.8012 (t) REVERT: B 219 HIS cc_start: 0.7031 (m90) cc_final: 0.6153 (t70) REVERT: B 280 THR cc_start: 0.7973 (m) cc_final: 0.7602 (t) outliers start: 10 outliers final: 7 residues processed: 174 average time/residue: 0.0809 time to fit residues: 17.5241 Evaluate side-chains 168 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 281 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 47 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.153033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.129946 restraints weight = 10167.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.133931 restraints weight = 6262.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.136667 restraints weight = 4347.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.138554 restraints weight = 3280.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.139864 restraints weight = 2646.313| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5136 Z= 0.201 Angle : 0.798 8.277 6974 Z= 0.412 Chirality : 0.050 0.202 790 Planarity : 0.007 0.066 881 Dihedral : 8.131 144.694 697 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.47 % Allowed : 19.50 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.31), residues: 621 helix: -1.32 (0.28), residues: 282 sheet: -3.29 (0.77), residues: 36 loop : -2.21 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 244 TYR 0.019 0.002 TYR B 49 PHE 0.043 0.002 PHE B 119 TRP 0.018 0.002 TRP B 58 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 5136) covalent geometry : angle 0.79776 ( 6974) hydrogen bonds : bond 0.04438 ( 167) hydrogen bonds : angle 5.11878 ( 489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7603 (m-80) cc_final: 0.6861 (m-80) REVERT: A 56 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7236 (pttt) REVERT: A 62 GLN cc_start: 0.7038 (mp10) cc_final: 0.6777 (mp10) REVERT: A 267 MET cc_start: 0.7233 (ttp) cc_final: 0.6981 (ttp) REVERT: A 298 ASP cc_start: 0.7325 (p0) cc_final: 0.7116 (p0) REVERT: B 66 GLN cc_start: 0.7665 (tp-100) cc_final: 0.7286 (tp-100) REVERT: B 122 LYS cc_start: 0.8283 (tptt) cc_final: 0.7456 (tptp) REVERT: B 125 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7348 (tm-30) REVERT: B 145 PHE cc_start: 0.7688 (t80) cc_final: 0.7254 (t80) REVERT: B 149 PHE cc_start: 0.7488 (m-80) cc_final: 0.7261 (m-80) REVERT: B 169 LEU cc_start: 0.7459 (tp) cc_final: 0.7043 (mt) REVERT: B 174 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: B 191 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7171 (ttt180) REVERT: B 219 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6263 (t70) REVERT: B 244 ARG cc_start: 0.7132 (ttp-110) cc_final: 0.6848 (ttp-110) REVERT: B 247 LYS cc_start: 0.8315 (mttp) cc_final: 0.8025 (mttp) REVERT: B 275 ASP cc_start: 0.5642 (t0) cc_final: 0.5393 (t0) outliers start: 18 outliers final: 7 residues processed: 186 average time/residue: 0.0787 time to fit residues: 18.0999 Evaluate side-chains 182 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 281 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.150609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.127390 restraints weight = 10107.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.131398 restraints weight = 6140.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.134119 restraints weight = 4215.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.136003 restraints weight = 3159.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137258 restraints weight = 2535.484| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5136 Z= 0.201 Angle : 0.768 9.284 6974 Z= 0.393 Chirality : 0.051 0.204 790 Planarity : 0.007 0.067 881 Dihedral : 7.566 126.761 697 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.86 % Allowed : 24.13 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.31), residues: 621 helix: -1.18 (0.28), residues: 287 sheet: -2.72 (0.88), residues: 33 loop : -2.21 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 227 TYR 0.032 0.002 TYR A 204 PHE 0.034 0.002 PHE B 119 TRP 0.018 0.002 TRP B 58 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 5136) covalent geometry : angle 0.76837 ( 6974) hydrogen bonds : bond 0.04514 ( 167) hydrogen bonds : angle 5.02161 ( 489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7636 (m-80) cc_final: 0.7040 (m-80) REVERT: A 20 VAL cc_start: 0.7589 (t) cc_final: 0.7108 (p) REVERT: A 33 ILE cc_start: 0.8098 (pt) cc_final: 0.7622 (mm) REVERT: A 56 LYS cc_start: 0.7548 (ptmm) cc_final: 0.7174 (pttt) REVERT: A 89 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7308 (t0) REVERT: A 110 MET cc_start: 0.7743 (mmm) cc_final: 0.7343 (tpt) REVERT: A 115 ARG cc_start: 0.7332 (mtt180) cc_final: 0.6726 (mtp180) REVERT: A 177 PHE cc_start: 0.6321 (m-80) cc_final: 0.6037 (t80) REVERT: A 267 MET cc_start: 0.7281 (ttp) cc_final: 0.7015 (ttp) REVERT: A 278 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7270 (ttm170) REVERT: B 66 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7297 (tp-100) REVERT: B 112 GLU cc_start: 0.7168 (tt0) cc_final: 0.5610 (tp30) REVERT: B 125 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 145 PHE cc_start: 0.7818 (t80) cc_final: 0.7224 (t80) REVERT: B 149 PHE cc_start: 0.7609 (m-80) cc_final: 0.7316 (m-80) REVERT: B 156 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6512 (pm20) REVERT: B 169 LEU cc_start: 0.7470 (tp) cc_final: 0.7186 (mt) REVERT: B 191 ARG cc_start: 0.7867 (ttt180) cc_final: 0.7157 (ttt180) REVERT: B 219 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6323 (t70) REVERT: B 244 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.7024 (ttp-110) REVERT: B 247 LYS cc_start: 0.8352 (mttp) cc_final: 0.8050 (mttp) outliers start: 20 outliers final: 10 residues processed: 180 average time/residue: 0.0781 time to fit residues: 17.4509 Evaluate side-chains 186 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.0020 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.152404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129444 restraints weight = 10069.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.133443 restraints weight = 6084.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.136261 restraints weight = 4150.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.138200 restraints weight = 3091.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.139529 restraints weight = 2459.847| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5136 Z= 0.145 Angle : 0.731 9.827 6974 Z= 0.369 Chirality : 0.049 0.219 790 Planarity : 0.006 0.065 881 Dihedral : 7.024 113.135 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.67 % Allowed : 26.45 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.32), residues: 621 helix: -0.92 (0.29), residues: 293 sheet: -2.89 (0.86), residues: 30 loop : -2.22 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.049 0.002 TYR A 204 PHE 0.022 0.002 PHE B 119 TRP 0.011 0.001 TRP B 58 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5136) covalent geometry : angle 0.73143 ( 6974) hydrogen bonds : bond 0.04082 ( 167) hydrogen bonds : angle 4.85641 ( 489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7555 (m-80) cc_final: 0.7015 (m-80) REVERT: A 89 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7191 (t0) REVERT: A 110 MET cc_start: 0.7709 (mmm) cc_final: 0.6963 (mmm) REVERT: A 114 LEU cc_start: 0.8523 (mm) cc_final: 0.7905 (mm) REVERT: A 115 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6851 (mtp180) REVERT: A 121 HIS cc_start: 0.7790 (m90) cc_final: 0.7272 (m90) REVERT: A 171 ARG cc_start: 0.7201 (ttm110) cc_final: 0.6869 (ttm110) REVERT: A 267 MET cc_start: 0.7255 (ttp) cc_final: 0.6980 (ttp) REVERT: A 278 ARG cc_start: 0.7486 (ttm170) cc_final: 0.7266 (ttm170) REVERT: B 66 GLN cc_start: 0.7628 (tp-100) cc_final: 0.7237 (tp-100) REVERT: B 112 GLU cc_start: 0.7177 (tt0) cc_final: 0.5609 (tp30) REVERT: B 125 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 145 PHE cc_start: 0.7738 (t80) cc_final: 0.7071 (t80) REVERT: B 149 PHE cc_start: 0.7554 (m-80) cc_final: 0.7280 (m-80) REVERT: B 156 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: B 169 LEU cc_start: 0.7477 (tp) cc_final: 0.7218 (mt) REVERT: B 219 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6243 (t70) REVERT: B 244 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.7003 (ttp-110) REVERT: B 247 LYS cc_start: 0.8329 (mttp) cc_final: 0.8023 (mttp) REVERT: B 275 ASP cc_start: 0.5679 (t0) cc_final: 0.5361 (t0) outliers start: 19 outliers final: 13 residues processed: 176 average time/residue: 0.0755 time to fit residues: 16.6661 Evaluate side-chains 183 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 268 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.0050 chunk 1 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.154288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.131238 restraints weight = 10224.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.135335 restraints weight = 6205.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.138152 restraints weight = 4226.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140045 restraints weight = 3138.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.141476 restraints weight = 2498.431| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4151 r_free = 0.4151 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4151 r_free = 0.4151 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5136 Z= 0.134 Angle : 0.725 11.002 6974 Z= 0.359 Chirality : 0.048 0.237 790 Planarity : 0.006 0.061 881 Dihedral : 6.691 105.589 697 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.86 % Allowed : 26.83 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.32), residues: 621 helix: -0.73 (0.30), residues: 294 sheet: -3.03 (0.83), residues: 30 loop : -2.14 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.036 0.002 TYR A 204 PHE 0.023 0.002 PHE A 266 TRP 0.011 0.001 TRP A 229 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5136) covalent geometry : angle 0.72528 ( 6974) hydrogen bonds : bond 0.03899 ( 167) hydrogen bonds : angle 4.76841 ( 489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7460 (m-80) cc_final: 0.7036 (m-80) REVERT: A 89 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7097 (t0) REVERT: A 110 MET cc_start: 0.7722 (mmm) cc_final: 0.6828 (mmm) REVERT: A 114 LEU cc_start: 0.8489 (mm) cc_final: 0.7802 (mm) REVERT: A 115 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6836 (mtp180) REVERT: A 121 HIS cc_start: 0.7716 (m90) cc_final: 0.7274 (m90) REVERT: A 250 ASP cc_start: 0.7317 (t0) cc_final: 0.7083 (t0) REVERT: A 267 MET cc_start: 0.7273 (ttp) cc_final: 0.7001 (ttp) REVERT: B 66 GLN cc_start: 0.7592 (tp-100) cc_final: 0.7180 (tp-100) REVERT: B 112 GLU cc_start: 0.7156 (tt0) cc_final: 0.5592 (tp30) REVERT: B 125 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 145 PHE cc_start: 0.7715 (t80) cc_final: 0.6987 (t80) REVERT: B 149 PHE cc_start: 0.7563 (m-80) cc_final: 0.7227 (m-80) REVERT: B 156 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: B 169 LEU cc_start: 0.7443 (tp) cc_final: 0.7200 (mt) REVERT: B 219 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6223 (t70) REVERT: B 244 ARG cc_start: 0.7247 (ttp-110) cc_final: 0.6993 (ttp-110) REVERT: B 247 LYS cc_start: 0.8341 (mttp) cc_final: 0.8029 (mttp) REVERT: B 275 ASP cc_start: 0.5523 (t0) cc_final: 0.5185 (t0) REVERT: B 331 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7958 (mtmm) REVERT: B 334 THR cc_start: 0.8350 (t) cc_final: 0.7987 (p) REVERT: B 336 ILE cc_start: 0.6942 (mm) cc_final: 0.6646 (tt) REVERT: B 338 GLU cc_start: 0.7047 (pp20) cc_final: 0.6771 (pp20) outliers start: 20 outliers final: 14 residues processed: 185 average time/residue: 0.0715 time to fit residues: 16.7592 Evaluate side-chains 193 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 268 CYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 281 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.152877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.129833 restraints weight = 10104.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.133917 restraints weight = 6164.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.136727 restraints weight = 4218.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.138750 restraints weight = 3140.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.140043 restraints weight = 2484.635| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5136 Z= 0.146 Angle : 0.751 13.115 6974 Z= 0.371 Chirality : 0.049 0.231 790 Planarity : 0.006 0.054 881 Dihedral : 6.548 98.890 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.63 % Allowed : 28.57 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.32), residues: 621 helix: -0.66 (0.30), residues: 301 sheet: -2.97 (0.81), residues: 30 loop : -2.18 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 278 TYR 0.024 0.002 TYR A 204 PHE 0.016 0.002 PHE B 119 TRP 0.011 0.001 TRP B 58 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5136) covalent geometry : angle 0.75077 ( 6974) hydrogen bonds : bond 0.03927 ( 167) hydrogen bonds : angle 4.87265 ( 489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7461 (m-80) cc_final: 0.7141 (m-80) REVERT: A 55 VAL cc_start: 0.7630 (m) cc_final: 0.7427 (p) REVERT: A 57 TYR cc_start: 0.7751 (m-10) cc_final: 0.7338 (m-80) REVERT: A 89 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7136 (t0) REVERT: A 114 LEU cc_start: 0.8498 (mm) cc_final: 0.8161 (mm) REVERT: A 115 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6870 (mtp180) REVERT: A 121 HIS cc_start: 0.7762 (m90) cc_final: 0.7357 (m90) REVERT: A 171 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6831 (ttm110) REVERT: A 214 MET cc_start: 0.7758 (ttm) cc_final: 0.7498 (ttm) REVERT: A 267 MET cc_start: 0.7344 (ttp) cc_final: 0.7086 (ttp) REVERT: A 278 ARG cc_start: 0.7303 (ttm170) cc_final: 0.7063 (ttm170) REVERT: B 66 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7188 (tp-100) REVERT: B 112 GLU cc_start: 0.7167 (tt0) cc_final: 0.5634 (tp30) REVERT: B 125 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 145 PHE cc_start: 0.7698 (t80) cc_final: 0.6953 (t80) REVERT: B 149 PHE cc_start: 0.7573 (m-80) cc_final: 0.7205 (m-80) REVERT: B 156 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: B 169 LEU cc_start: 0.7456 (tp) cc_final: 0.7207 (mt) REVERT: B 219 HIS cc_start: 0.6979 (OUTLIER) cc_final: 0.6173 (t70) REVERT: B 244 ARG cc_start: 0.7172 (ttp-110) cc_final: 0.6924 (ttp-110) REVERT: B 247 LYS cc_start: 0.8354 (mttp) cc_final: 0.8036 (mttp) REVERT: B 331 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7958 (mtmm) REVERT: B 334 THR cc_start: 0.8342 (t) cc_final: 0.8000 (p) REVERT: B 336 ILE cc_start: 0.6999 (mm) cc_final: 0.6752 (tt) REVERT: B 338 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6752 (pp20) outliers start: 24 outliers final: 15 residues processed: 186 average time/residue: 0.0770 time to fit residues: 17.9943 Evaluate side-chains 193 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.155222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.131668 restraints weight = 10073.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.135830 restraints weight = 6167.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.138654 restraints weight = 4230.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.140634 restraints weight = 3154.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.141961 restraints weight = 2511.467| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4155 r_free = 0.4155 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4155 r_free = 0.4155 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5136 Z= 0.136 Angle : 0.765 15.242 6974 Z= 0.376 Chirality : 0.049 0.234 790 Planarity : 0.005 0.053 881 Dihedral : 6.401 94.193 697 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.67 % Allowed : 29.34 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.32), residues: 621 helix: -0.60 (0.30), residues: 295 sheet: -2.96 (0.82), residues: 30 loop : -2.09 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.038 0.002 TYR A 204 PHE 0.016 0.001 PHE A 235 TRP 0.012 0.001 TRP A 229 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5136) covalent geometry : angle 0.76476 ( 6974) hydrogen bonds : bond 0.03754 ( 167) hydrogen bonds : angle 4.81155 ( 489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7351 (m-80) cc_final: 0.7047 (m-80) REVERT: A 110 MET cc_start: 0.7789 (mmm) cc_final: 0.7318 (tpt) REVERT: A 114 LEU cc_start: 0.8426 (mm) cc_final: 0.8198 (mm) REVERT: A 115 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6711 (mtp85) REVERT: A 158 HIS cc_start: 0.7740 (p-80) cc_final: 0.7523 (p-80) REVERT: A 171 ARG cc_start: 0.7343 (ttm110) cc_final: 0.6753 (ttm110) REVERT: A 267 MET cc_start: 0.7345 (ttp) cc_final: 0.7119 (ttp) REVERT: A 278 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7167 (ttm170) REVERT: B 66 GLN cc_start: 0.7595 (tp-100) cc_final: 0.7168 (tp-100) REVERT: B 112 GLU cc_start: 0.7177 (tt0) cc_final: 0.5690 (tp30) REVERT: B 122 LYS cc_start: 0.8408 (tptt) cc_final: 0.7535 (tptp) REVERT: B 125 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7247 (tm-30) REVERT: B 145 PHE cc_start: 0.7664 (t80) cc_final: 0.6877 (t80) REVERT: B 149 PHE cc_start: 0.7543 (m-80) cc_final: 0.7182 (m-80) REVERT: B 169 LEU cc_start: 0.7427 (tp) cc_final: 0.7169 (mt) REVERT: B 219 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6154 (t70) REVERT: B 248 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7482 (mtp85) REVERT: B 331 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7951 (mtmm) REVERT: B 334 THR cc_start: 0.8307 (t) cc_final: 0.8011 (p) REVERT: B 336 ILE cc_start: 0.6970 (mm) cc_final: 0.6674 (tt) outliers start: 19 outliers final: 14 residues processed: 178 average time/residue: 0.0748 time to fit residues: 16.7964 Evaluate side-chains 182 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 14 optimal weight: 0.0270 chunk 25 optimal weight: 0.0270 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.156335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133083 restraints weight = 9899.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.137177 restraints weight = 6025.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.139991 restraints weight = 4127.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.141982 restraints weight = 3078.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.143403 restraints weight = 2443.804| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4173 r_free = 0.4173 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4173 r_free = 0.4173 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5136 Z= 0.133 Angle : 0.768 16.211 6974 Z= 0.377 Chirality : 0.048 0.229 790 Planarity : 0.006 0.053 881 Dihedral : 6.303 91.160 697 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.09 % Allowed : 31.47 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.32), residues: 621 helix: -0.43 (0.31), residues: 289 sheet: -2.93 (0.84), residues: 30 loop : -2.02 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 244 TYR 0.027 0.002 TYR A 204 PHE 0.018 0.001 PHE A 235 TRP 0.055 0.003 TRP B 58 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5136) covalent geometry : angle 0.76816 ( 6974) hydrogen bonds : bond 0.03712 ( 167) hydrogen bonds : angle 4.77741 ( 489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7319 (m-80) cc_final: 0.7104 (m-80) REVERT: A 110 MET cc_start: 0.7807 (mmm) cc_final: 0.7227 (tpt) REVERT: A 114 LEU cc_start: 0.8393 (mm) cc_final: 0.8082 (mm) REVERT: A 115 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6628 (mtp85) REVERT: A 123 ASN cc_start: 0.6709 (m-40) cc_final: 0.6397 (m-40) REVERT: A 158 HIS cc_start: 0.7704 (p-80) cc_final: 0.7495 (p-80) REVERT: A 171 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6897 (ttm110) REVERT: A 215 GLU cc_start: 0.7566 (mp0) cc_final: 0.6851 (mp0) REVERT: A 267 MET cc_start: 0.7242 (ttp) cc_final: 0.7032 (ttp) REVERT: B 66 GLN cc_start: 0.7543 (tp-100) cc_final: 0.7067 (tp-100) REVERT: B 112 GLU cc_start: 0.7174 (tt0) cc_final: 0.5707 (tp30) REVERT: B 122 LYS cc_start: 0.8395 (tptt) cc_final: 0.7475 (tptp) REVERT: B 125 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 145 PHE cc_start: 0.7575 (t80) cc_final: 0.6711 (t80) REVERT: B 149 PHE cc_start: 0.7432 (m-80) cc_final: 0.7083 (m-80) REVERT: B 152 ASN cc_start: 0.6420 (p0) cc_final: 0.6101 (p0) REVERT: B 155 MET cc_start: 0.6059 (ptt) cc_final: 0.5783 (ptt) REVERT: B 169 LEU cc_start: 0.7463 (tp) cc_final: 0.7198 (mt) REVERT: B 219 HIS cc_start: 0.6896 (OUTLIER) cc_final: 0.6118 (t70) REVERT: B 247 LYS cc_start: 0.8374 (mttp) cc_final: 0.8059 (mttp) REVERT: B 248 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7438 (mtp85) REVERT: B 331 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7968 (mtmm) REVERT: B 334 THR cc_start: 0.8289 (t) cc_final: 0.7972 (p) REVERT: B 336 ILE cc_start: 0.6935 (mm) cc_final: 0.6653 (tt) REVERT: B 338 GLU cc_start: 0.7090 (pp20) cc_final: 0.6830 (pp20) outliers start: 16 outliers final: 15 residues processed: 181 average time/residue: 0.0735 time to fit residues: 16.8619 Evaluate side-chains 190 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 27 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.155643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.132179 restraints weight = 10075.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.136312 restraints weight = 6154.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.139173 restraints weight = 4223.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.141079 restraints weight = 3146.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.142571 restraints weight = 2517.122| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5136 Z= 0.138 Angle : 0.767 15.391 6974 Z= 0.379 Chirality : 0.048 0.233 790 Planarity : 0.006 0.053 881 Dihedral : 6.316 88.483 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.67 % Allowed : 31.85 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.33), residues: 621 helix: -0.44 (0.30), residues: 296 sheet: -2.89 (0.85), residues: 30 loop : -2.03 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 244 TYR 0.024 0.002 TYR A 204 PHE 0.026 0.002 PHE A 177 TRP 0.068 0.004 TRP B 58 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5136) covalent geometry : angle 0.76670 ( 6974) hydrogen bonds : bond 0.03832 ( 167) hydrogen bonds : angle 4.84022 ( 489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7799 (mmm) cc_final: 0.7276 (tpt) REVERT: A 114 LEU cc_start: 0.8397 (mm) cc_final: 0.8151 (mm) REVERT: A 115 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6655 (mtp85) REVERT: A 123 ASN cc_start: 0.6683 (m-40) cc_final: 0.6412 (m-40) REVERT: A 158 HIS cc_start: 0.7764 (p-80) cc_final: 0.7554 (p-80) REVERT: A 171 ARG cc_start: 0.7416 (ttm110) cc_final: 0.6869 (ttm110) REVERT: A 215 GLU cc_start: 0.7657 (mp0) cc_final: 0.6965 (mp0) REVERT: B 66 GLN cc_start: 0.7573 (tp-100) cc_final: 0.7106 (tp-100) REVERT: B 112 GLU cc_start: 0.7178 (tt0) cc_final: 0.5710 (tp30) REVERT: B 122 LYS cc_start: 0.8373 (tptt) cc_final: 0.7467 (tptp) REVERT: B 125 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 145 PHE cc_start: 0.7668 (t80) cc_final: 0.6761 (t80) REVERT: B 149 PHE cc_start: 0.7537 (m-80) cc_final: 0.7189 (m-80) REVERT: B 152 ASN cc_start: 0.6397 (p0) cc_final: 0.6037 (p0) REVERT: B 169 LEU cc_start: 0.7407 (tp) cc_final: 0.7131 (mt) REVERT: B 219 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6139 (t70) REVERT: B 244 ARG cc_start: 0.6900 (ttp-110) cc_final: 0.6663 (ttp-110) REVERT: B 248 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7523 (mtp85) REVERT: B 331 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7959 (mtmm) REVERT: B 334 THR cc_start: 0.8276 (t) cc_final: 0.7954 (p) REVERT: B 336 ILE cc_start: 0.6893 (mm) cc_final: 0.6606 (tt) REVERT: B 338 GLU cc_start: 0.7063 (pp20) cc_final: 0.6775 (pp20) outliers start: 19 outliers final: 16 residues processed: 184 average time/residue: 0.0741 time to fit residues: 17.2012 Evaluate side-chains 191 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.153751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.130029 restraints weight = 10227.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.134199 restraints weight = 6223.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.137057 restraints weight = 4259.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.138930 restraints weight = 3179.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.140332 restraints weight = 2553.785| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5136 Z= 0.149 Angle : 0.777 14.921 6974 Z= 0.383 Chirality : 0.049 0.231 790 Planarity : 0.006 0.053 881 Dihedral : 6.346 86.195 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.05 % Allowed : 31.85 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.33), residues: 621 helix: -0.50 (0.30), residues: 302 sheet: -2.90 (0.84), residues: 30 loop : -2.03 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 56 TYR 0.024 0.002 TYR A 204 PHE 0.019 0.002 PHE A 177 TRP 0.011 0.001 TRP B 58 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5136) covalent geometry : angle 0.77748 ( 6974) hydrogen bonds : bond 0.04092 ( 167) hydrogen bonds : angle 4.86037 ( 489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1133.79 seconds wall clock time: 20 minutes 10.05 seconds (1210.05 seconds total)