Starting phenix.real_space_refine on Thu Mar 6 06:20:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xi8_22191/03_2025/6xi8_22191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xi8_22191/03_2025/6xi8_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_2025/6xi8_22191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xi8_22191/03_2025/6xi8_22191.map" model { file = "/net/cci-nas-00/data/ceres_data/6xi8_22191/03_2025/6xi8_22191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xi8_22191/03_2025/6xi8_22191.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} 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: 3.76, per 1000 atoms: 0.75 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: 1.22 Conformation dependent library (CDL) restraints added in 673.7 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: 0.51 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: 1.11 Time building geometry restraints manager: 1.47 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- 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= 0.650 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 : 6.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.105 0.006 TRP B 58 HIS 0.008 0.001 HIS A 121 PHE 0.028 0.003 PHE B 177 TYR 0.056 0.003 TYR A 57 ARG 0.013 0.001 ARG B 50 *********************** 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 : 0.546 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: 0.6933 (pttt) REVERT: A 266 PHE cc_start: 0.7276 (p90) cc_final: 0.6101 (p90) REVERT: B 122 LYS cc_start: 0.7715 (tptt) cc_final: 0.7086 (tptp) REVERT: B 145 PHE cc_start: 0.6492 (t80) cc_final: 0.5935 (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: 0.2106 time to fit residues: 47.5847 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 : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.157439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133941 restraints weight = 10082.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.137959 restraints weight = 6230.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140729 restraints weight = 4329.818| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5136 Z= 0.216 Angle : 0.811 11.082 6974 Z= 0.405 Chirality : 0.050 0.264 790 Planarity : 0.008 0.069 881 Dihedral : 8.816 161.165 697 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.32 % Allowed : 13.13 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.30), residues: 621 helix: -1.84 (0.27), residues: 281 sheet: -2.82 (0.84), residues: 33 loop : -2.27 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 58 HIS 0.003 0.001 HIS B 213 PHE 0.019 0.002 PHE A 266 TYR 0.018 0.002 TYR B 261 ARG 0.006 0.000 ARG B 244 *********************** 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 188 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 ARG cc_start: 0.6816 (mtm180) cc_final: 0.6602 (mtm110) REVERT: A 61 MET cc_start: 0.6957 (mmt) cc_final: 0.6683 (mmm) REVERT: A 65 ASN cc_start: 0.6828 (p0) cc_final: 0.6159 (p0) REVERT: A 144 LYS cc_start: 0.7352 (mmtt) cc_final: 0.6881 (mmtt) REVERT: A 266 PHE cc_start: 0.7943 (p90) cc_final: 0.7366 (p90) REVERT: B 66 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7224 (tp-100) REVERT: B 110 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5512 (tpt) REVERT: B 122 LYS cc_start: 0.8216 (tptt) cc_final: 0.7923 (tptt) REVERT: B 125 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 145 PHE cc_start: 0.7527 (t80) cc_final: 0.6973 (t80) REVERT: B 169 LEU cc_start: 0.7351 (tp) cc_final: 0.6869 (tp) REVERT: B 173 SER cc_start: 0.8261 (t) cc_final: 0.8027 (t) REVERT: B 219 HIS cc_start: 0.7042 (m90) cc_final: 0.6158 (t70) outliers start: 12 outliers final: 8 residues processed: 179 average time/residue: 0.2358 time to fit residues: 51.9131 Evaluate side-chains 176 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 62 LYS Chi-restraints excluded: chain B residue 110 MET 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 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.153371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.130096 restraints weight = 10217.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.134222 restraints weight = 6209.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.136990 restraints weight = 4275.655| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5136 Z= 0.249 Angle : 0.771 9.056 6974 Z= 0.394 Chirality : 0.049 0.200 790 Planarity : 0.007 0.070 881 Dihedral : 8.099 145.432 697 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.28 % Allowed : 20.66 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.31), residues: 621 helix: -1.30 (0.28), residues: 282 sheet: -2.41 (0.92), residues: 28 loop : -2.23 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 58 HIS 0.005 0.001 HIS A 63 PHE 0.025 0.002 PHE A 266 TYR 0.014 0.002 TYR B 49 ARG 0.003 0.001 ARG A 168 *********************** 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 199 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7558 (m-80) cc_final: 0.6690 (m-80) REVERT: A 56 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7250 (pttt) REVERT: A 177 PHE cc_start: 0.6402 (m-80) cc_final: 0.5940 (t80) REVERT: A 237 THR cc_start: 0.6087 (m) cc_final: 0.5821 (p) REVERT: A 266 PHE cc_start: 0.7965 (p90) cc_final: 0.7491 (p90) REVERT: A 267 MET cc_start: 0.7282 (ttp) cc_final: 0.7011 (ttp) REVERT: A 298 ASP cc_start: 0.7312 (p0) cc_final: 0.7108 (p0) REVERT: B 66 GLN cc_start: 0.7666 (tp-100) cc_final: 0.7281 (tp-100) REVERT: B 112 GLU cc_start: 0.7372 (tt0) cc_final: 0.6135 (tp30) REVERT: B 115 ASP cc_start: 0.7181 (p0) cc_final: 0.6746 (p0) REVERT: B 122 LYS cc_start: 0.8271 (tptt) cc_final: 0.7948 (tptt) REVERT: B 125 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 145 PHE cc_start: 0.7652 (t80) cc_final: 0.7200 (t80) REVERT: B 149 PHE cc_start: 0.7541 (m-80) cc_final: 0.7272 (m-80) REVERT: B 169 LEU cc_start: 0.7462 (tp) cc_final: 0.7053 (mt) REVERT: B 174 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: B 191 ARG cc_start: 0.7975 (ttt180) cc_final: 0.7205 (ttt180) REVERT: B 219 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6213 (t70) REVERT: B 248 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7312 (mtp85) REVERT: B 275 ASP cc_start: 0.5705 (t0) cc_final: 0.5386 (t0) outliers start: 17 outliers final: 5 residues processed: 189 average time/residue: 0.2437 time to fit residues: 57.0359 Evaluate side-chains 185 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 HIS ** 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 = 0.4295 r_free = 0.4295 target = 0.153125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.130087 restraints weight = 10132.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.134179 restraints weight = 6111.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.136975 restraints weight = 4157.121| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5136 Z= 0.229 Angle : 0.732 8.229 6974 Z= 0.375 Chirality : 0.050 0.204 790 Planarity : 0.006 0.062 881 Dihedral : 7.456 127.878 697 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.05 % Allowed : 22.59 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.31), residues: 621 helix: -1.11 (0.29), residues: 287 sheet: -2.45 (0.90), residues: 28 loop : -2.27 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 58 HIS 0.006 0.001 HIS A 121 PHE 0.014 0.001 PHE A 266 TYR 0.024 0.002 TYR A 204 ARG 0.006 0.001 ARG A 227 *********************** 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 187 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7516 (m-80) cc_final: 0.6856 (m-80) REVERT: A 33 ILE cc_start: 0.8119 (pt) cc_final: 0.7644 (mm) REVERT: A 89 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7167 (t0) REVERT: A 110 MET cc_start: 0.7714 (mmm) cc_final: 0.6976 (mmm) REVERT: A 114 LEU cc_start: 0.8544 (mm) cc_final: 0.8080 (mm) REVERT: A 115 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6566 (mtp180) REVERT: A 117 VAL cc_start: 0.8207 (p) cc_final: 0.7977 (t) REVERT: A 267 MET cc_start: 0.7251 (ttp) cc_final: 0.6967 (ttp) REVERT: A 278 ARG cc_start: 0.7472 (ttm170) cc_final: 0.7237 (ttm170) REVERT: A 298 ASP cc_start: 0.7409 (p0) cc_final: 0.7187 (p0) REVERT: B 66 GLN cc_start: 0.7654 (tp-100) cc_final: 0.7303 (tp-100) REVERT: B 112 GLU cc_start: 0.7411 (tt0) cc_final: 0.6107 (tp30) REVERT: B 115 ASP cc_start: 0.7172 (p0) cc_final: 0.6725 (p0) REVERT: B 122 LYS cc_start: 0.8304 (tptt) cc_final: 0.7934 (tptt) REVERT: B 125 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7606 (tm-30) REVERT: B 145 PHE cc_start: 0.7642 (t80) cc_final: 0.7169 (t80) REVERT: B 149 PHE cc_start: 0.7536 (m-80) cc_final: 0.7256 (m-80) REVERT: B 156 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: B 169 LEU cc_start: 0.7474 (tp) cc_final: 0.7084 (mt) REVERT: B 191 ARG cc_start: 0.7904 (ttt180) cc_final: 0.7179 (ttt180) REVERT: B 218 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7476 (mm) REVERT: B 219 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6224 (t70) REVERT: B 244 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6903 (ttp-110) REVERT: B 247 LYS cc_start: 0.8336 (mttp) cc_final: 0.8027 (mttp) outliers start: 21 outliers final: 9 residues processed: 174 average time/residue: 0.2850 time to fit residues: 61.7825 Evaluate side-chains 175 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 89 ASP Chi-restraints excluded: chain A residue 236 MET 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 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 189 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 20 optimal weight: 0.0170 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 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 = 0.4315 r_free = 0.4315 target = 0.154549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.130762 restraints weight = 10124.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.134898 restraints weight = 6139.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.137770 restraints weight = 4185.786| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5136 Z= 0.188 Angle : 0.726 10.287 6974 Z= 0.361 Chirality : 0.048 0.181 790 Planarity : 0.006 0.067 881 Dihedral : 6.971 114.247 697 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.67 % Allowed : 24.90 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.32), residues: 621 helix: -0.91 (0.29), residues: 293 sheet: -2.98 (0.82), residues: 30 loop : -2.19 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.005 0.001 HIS A 121 PHE 0.016 0.001 PHE A 266 TYR 0.023 0.002 TYR A 204 ARG 0.003 0.000 ARG B 281 *********************** 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 183 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7449 (m-80) cc_final: 0.6927 (m-80) REVERT: A 33 ILE cc_start: 0.8168 (pt) cc_final: 0.7675 (mm) REVERT: A 57 TYR cc_start: 0.7747 (m-80) cc_final: 0.7437 (m-80) REVERT: A 89 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7148 (t0) REVERT: A 110 MET cc_start: 0.7721 (mmm) cc_final: 0.7503 (mmm) REVERT: A 114 LEU cc_start: 0.8480 (mm) cc_final: 0.8116 (mm) REVERT: A 115 ARG cc_start: 0.7336 (mtt180) cc_final: 0.6760 (mtp180) REVERT: A 121 HIS cc_start: 0.7772 (m90) cc_final: 0.7221 (m90) REVERT: A 177 PHE cc_start: 0.6253 (m-80) cc_final: 0.5936 (t80) REVERT: A 204 TYR cc_start: 0.6752 (t80) cc_final: 0.6537 (t80) REVERT: A 214 MET cc_start: 0.7901 (ttm) cc_final: 0.7622 (ttm) REVERT: B 66 GLN cc_start: 0.7626 (tp-100) cc_final: 0.7230 (tp-100) REVERT: B 122 LYS cc_start: 0.8299 (tptt) cc_final: 0.7914 (tptt) REVERT: B 125 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B 145 PHE cc_start: 0.7688 (t80) cc_final: 0.7143 (t80) REVERT: B 149 PHE cc_start: 0.7589 (m-80) cc_final: 0.7342 (m-80) REVERT: B 169 LEU cc_start: 0.7448 (tp) cc_final: 0.7053 (mt) REVERT: B 174 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7140 (pt0) REVERT: B 191 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7163 (ttt180) REVERT: B 209 LEU cc_start: 0.8038 (mt) cc_final: 0.6935 (tt) REVERT: B 219 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6225 (t70) REVERT: B 244 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.6990 (ttp-110) REVERT: B 247 LYS cc_start: 0.8334 (mttp) cc_final: 0.8020 (mttp) REVERT: B 275 ASP cc_start: 0.5622 (t0) cc_final: 0.5284 (t0) outliers start: 19 outliers final: 10 residues processed: 171 average time/residue: 0.2807 time to fit residues: 59.9754 Evaluate side-chains 177 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 174 GLU 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 28 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** 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 = 0.4333 r_free = 0.4333 target = 0.156023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.132769 restraints weight = 10064.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.136816 restraints weight = 6109.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.139648 restraints weight = 4180.388| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4129 r_free = 0.4129 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 = 0.4129 r_free = 0.4129 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4847 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= 0.183 Angle : 0.707 10.494 6974 Z= 0.351 Chirality : 0.047 0.218 790 Planarity : 0.006 0.064 881 Dihedral : 6.650 105.173 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.09 % Allowed : 27.80 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.32), residues: 621 helix: -0.65 (0.30), residues: 294 sheet: -3.17 (0.77), residues: 30 loop : -2.12 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 121 PHE 0.017 0.001 PHE B 222 TYR 0.018 0.001 TYR B 55 ARG 0.007 0.000 ARG A 278 *********************** 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 186 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7344 (m-80) cc_final: 0.6936 (m-80) REVERT: A 89 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6989 (t0) REVERT: A 110 MET cc_start: 0.7736 (mmm) cc_final: 0.7497 (mmm) REVERT: A 114 LEU cc_start: 0.8441 (mm) cc_final: 0.8066 (mm) REVERT: A 115 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6632 (mtp85) REVERT: A 121 HIS cc_start: 0.7688 (m90) cc_final: 0.7184 (m90) REVERT: A 171 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6735 (ttm110) REVERT: A 278 ARG cc_start: 0.7324 (ttm170) cc_final: 0.7064 (ttm170) REVERT: B 66 GLN cc_start: 0.7606 (tp-100) cc_final: 0.7175 (tp-100) REVERT: B 122 LYS cc_start: 0.8311 (tptt) cc_final: 0.7914 (tptt) REVERT: B 125 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7472 (tm-30) REVERT: B 145 PHE cc_start: 0.7619 (t80) cc_final: 0.7029 (t80) REVERT: B 149 PHE cc_start: 0.7529 (m-80) cc_final: 0.7246 (m-80) REVERT: B 156 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: B 169 LEU cc_start: 0.7419 (tp) cc_final: 0.6854 (mt) REVERT: B 174 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7130 (pt0) REVERT: B 191 ARG cc_start: 0.7861 (ttt180) cc_final: 0.7141 (ttt180) REVERT: B 219 HIS cc_start: 0.7031 (OUTLIER) cc_final: 0.6256 (t70) REVERT: B 247 LYS cc_start: 0.8319 (mttp) cc_final: 0.8003 (mttp) REVERT: B 275 ASP cc_start: 0.5552 (t0) cc_final: 0.5274 (t0) REVERT: B 334 THR cc_start: 0.8327 (t) cc_final: 0.7981 (p) REVERT: B 336 ILE cc_start: 0.6832 (mm) cc_final: 0.6527 (tt) REVERT: B 338 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6837 (pp20) outliers start: 16 outliers final: 7 residues processed: 176 average time/residue: 0.2824 time to fit residues: 62.6815 Evaluate side-chains 181 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE 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 156 GLN 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 245 CYS Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 chunk 2 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** 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 = 0.4321 r_free = 0.4321 target = 0.155290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.132151 restraints weight = 9944.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.136123 restraints weight = 6057.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.138943 restraints weight = 4147.632| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 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 = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.5126 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= 0.194 Angle : 0.742 13.539 6974 Z= 0.363 Chirality : 0.048 0.235 790 Planarity : 0.006 0.061 881 Dihedral : 6.469 98.047 697 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.44 % Allowed : 27.22 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.32), residues: 621 helix: -0.54 (0.30), residues: 290 sheet: -3.36 (0.73), residues: 30 loop : -2.09 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 58 HIS 0.004 0.001 HIS A 121 PHE 0.017 0.002 PHE B 222 TYR 0.019 0.001 TYR B 55 ARG 0.008 0.000 ARG B 244 *********************** 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 198 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7352 (m-80) cc_final: 0.7045 (m-80) REVERT: A 20 VAL cc_start: 0.7316 (t) cc_final: 0.6861 (p) REVERT: A 57 TYR cc_start: 0.7753 (m-80) cc_final: 0.7408 (m-80) REVERT: A 89 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.7043 (t0) REVERT: A 110 MET cc_start: 0.7752 (mmm) cc_final: 0.7506 (mmm) REVERT: A 114 LEU cc_start: 0.8428 (mm) cc_final: 0.8065 (mm) REVERT: A 115 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6782 (mtp85) REVERT: A 121 HIS cc_start: 0.7756 (m90) cc_final: 0.7292 (m90) REVERT: A 171 ARG cc_start: 0.7287 (ttm110) cc_final: 0.6734 (ttm110) REVERT: A 214 MET cc_start: 0.7803 (ttm) cc_final: 0.7527 (ttm) REVERT: A 267 MET cc_start: 0.7223 (ttp) cc_final: 0.6968 (ttp) REVERT: A 278 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7139 (ttm170) REVERT: B 66 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7157 (tp-100) REVERT: B 122 LYS cc_start: 0.8346 (tptt) cc_final: 0.7961 (tptt) REVERT: B 125 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 145 PHE cc_start: 0.7646 (t80) cc_final: 0.7006 (t80) REVERT: B 149 PHE cc_start: 0.7565 (m-80) cc_final: 0.7263 (m-80) REVERT: B 156 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6270 (pm20) REVERT: B 169 LEU cc_start: 0.7498 (tp) cc_final: 0.6892 (mt) REVERT: B 174 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: B 219 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6254 (t70) REVERT: B 244 ARG cc_start: 0.7086 (ttp-110) cc_final: 0.6688 (ttp-110) REVERT: B 247 LYS cc_start: 0.8373 (mttp) cc_final: 0.8044 (mttp) REVERT: B 275 ASP cc_start: 0.5589 (t0) cc_final: 0.5338 (t0) REVERT: B 334 THR cc_start: 0.8300 (t) cc_final: 0.7985 (p) outliers start: 23 outliers final: 13 residues processed: 183 average time/residue: 0.1832 time to fit residues: 41.8138 Evaluate side-chains 189 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain A residue 12 LYS 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 123 ASN Chi-restraints excluded: chain B residue 115 ASP 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 162 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 0.0670 chunk 45 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 25 optimal weight: 0.0020 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.156967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.133663 restraints weight = 10112.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.137765 restraints weight = 6152.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.140635 restraints weight = 4198.854| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 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 = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.5289 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= 0.188 Angle : 0.755 15.029 6974 Z= 0.369 Chirality : 0.048 0.228 790 Planarity : 0.006 0.059 881 Dihedral : 6.386 94.221 697 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.09 % Allowed : 29.34 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.32), residues: 621 helix: -0.56 (0.30), residues: 290 sheet: -3.32 (0.73), residues: 30 loop : -2.11 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP B 58 HIS 0.003 0.001 HIS A 121 PHE 0.014 0.001 PHE B 222 TYR 0.020 0.001 TYR B 55 ARG 0.006 0.000 ARG B 244 *********************** 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 187 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7294 (m-80) cc_final: 0.6977 (m-80) REVERT: A 20 VAL cc_start: 0.7265 (t) cc_final: 0.6827 (p) REVERT: A 57 TYR cc_start: 0.7745 (m-80) cc_final: 0.7369 (m-80) REVERT: A 65 ASN cc_start: 0.6443 (p0) cc_final: 0.5424 (p0) REVERT: A 89 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6670 (t0) REVERT: A 110 MET cc_start: 0.7726 (mmm) cc_final: 0.7462 (mmm) REVERT: A 114 LEU cc_start: 0.8386 (mm) cc_final: 0.8027 (mm) REVERT: A 115 ARG cc_start: 0.7158 (mtt180) cc_final: 0.6614 (mtp85) REVERT: A 144 LYS cc_start: 0.7372 (mmtt) cc_final: 0.7014 (mmtt) REVERT: A 158 HIS cc_start: 0.7623 (p-80) cc_final: 0.7399 (p-80) REVERT: A 171 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6725 (ttm110) REVERT: A 238 TYR cc_start: 0.6648 (t80) cc_final: 0.6445 (t80) REVERT: A 267 MET cc_start: 0.7183 (ttp) cc_final: 0.6935 (ttp) REVERT: A 278 ARG cc_start: 0.7437 (ttm170) cc_final: 0.7217 (ttm170) REVERT: B 66 GLN cc_start: 0.7574 (tp-100) cc_final: 0.7131 (tp-100) REVERT: B 122 LYS cc_start: 0.8339 (tptt) cc_final: 0.7955 (tptt) REVERT: B 125 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7456 (tm-30) REVERT: B 145 PHE cc_start: 0.7597 (t80) cc_final: 0.6940 (t80) REVERT: B 149 PHE cc_start: 0.7576 (m-80) cc_final: 0.7234 (m-80) REVERT: B 169 LEU cc_start: 0.7459 (tp) cc_final: 0.6871 (mt) REVERT: B 219 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6226 (t70) REVERT: B 244 ARG cc_start: 0.7123 (ttp-110) cc_final: 0.6861 (ttp-110) REVERT: B 248 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7516 (mmp80) REVERT: B 280 THR cc_start: 0.8172 (m) cc_final: 0.7885 (t) REVERT: B 331 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7893 (mtmm) REVERT: B 334 THR cc_start: 0.8300 (t) cc_final: 0.8004 (p) outliers start: 16 outliers final: 8 residues processed: 178 average time/residue: 0.1841 time to fit residues: 40.9796 Evaluate side-chains 180 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE 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 162 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 27 optimal weight: 0.0000 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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** ** 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 = 0.4320 r_free = 0.4320 target = 0.155348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.132271 restraints weight = 9949.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.136378 restraints weight = 5999.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.139166 restraints weight = 4075.197| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 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 = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5136 Z= 0.215 Angle : 0.773 15.114 6974 Z= 0.378 Chirality : 0.049 0.235 790 Planarity : 0.006 0.054 881 Dihedral : 6.355 89.532 697 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.47 % Allowed : 28.57 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.32), residues: 621 helix: -0.55 (0.30), residues: 293 sheet: -3.47 (0.69), residues: 30 loop : -2.07 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.025 0.002 PHE A 235 TYR 0.020 0.001 TYR B 55 ARG 0.007 0.001 ARG B 146 *********************** 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 195 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7383 (m-80) cc_final: 0.7168 (m-80) REVERT: A 20 VAL cc_start: 0.7267 (t) cc_final: 0.6796 (p) REVERT: A 57 TYR cc_start: 0.7741 (m-80) cc_final: 0.7361 (m-80) REVERT: A 89 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6688 (t0) REVERT: A 110 MET cc_start: 0.7720 (mmm) cc_final: 0.7441 (mmm) REVERT: A 114 LEU cc_start: 0.8412 (mm) cc_final: 0.8035 (mm) REVERT: A 115 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6812 (mtp180) REVERT: A 121 HIS cc_start: 0.7740 (m90) cc_final: 0.7294 (m90) REVERT: A 144 LYS cc_start: 0.7410 (mmtt) cc_final: 0.7063 (mmtt) REVERT: A 158 HIS cc_start: 0.7677 (p-80) cc_final: 0.7447 (p-80) REVERT: A 171 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6765 (ttm110) REVERT: A 215 GLU cc_start: 0.7689 (mp0) cc_final: 0.6992 (mp0) REVERT: A 238 TYR cc_start: 0.6658 (t80) cc_final: 0.6424 (t80) REVERT: A 278 ARG cc_start: 0.7382 (ttm170) cc_final: 0.7171 (ttm170) REVERT: B 66 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7124 (tp-100) REVERT: B 122 LYS cc_start: 0.8338 (tptt) cc_final: 0.7961 (tptt) REVERT: B 125 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 145 PHE cc_start: 0.7591 (t80) cc_final: 0.6943 (t80) REVERT: B 149 PHE cc_start: 0.7548 (m-80) cc_final: 0.7236 (m-80) REVERT: B 169 LEU cc_start: 0.7519 (tp) cc_final: 0.6890 (mt) REVERT: B 219 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6125 (t70) REVERT: B 244 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6795 (ttp-110) REVERT: B 248 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7458 (mtp85) REVERT: B 280 THR cc_start: 0.8203 (m) cc_final: 0.7883 (t) REVERT: B 334 THR cc_start: 0.8287 (t) cc_final: 0.7995 (p) REVERT: B 336 ILE cc_start: 0.6840 (mm) cc_final: 0.6610 (tt) outliers start: 18 outliers final: 11 residues processed: 184 average time/residue: 0.2524 time to fit residues: 58.0383 Evaluate side-chains 189 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** 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 = 0.153196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.129439 restraints weight = 10078.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.133575 restraints weight = 6019.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.136392 restraints weight = 4110.645| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5136 Z= 0.234 Angle : 0.787 14.326 6974 Z= 0.387 Chirality : 0.050 0.231 790 Planarity : 0.006 0.053 881 Dihedral : 6.423 85.156 697 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.67 % Allowed : 29.15 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.32), residues: 621 helix: -0.69 (0.29), residues: 306 sheet: -3.64 (0.68), residues: 30 loop : -2.19 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 58 HIS 0.006 0.001 HIS A 121 PHE 0.016 0.002 PHE A 266 TYR 0.017 0.001 TYR B 55 ARG 0.005 0.000 ARG B 244 ********************** 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 : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.7321 (t) cc_final: 0.6830 (p) REVERT: A 65 ASN cc_start: 0.6572 (p0) cc_final: 0.5813 (p0) REVERT: A 89 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7180 (t0) REVERT: A 114 LEU cc_start: 0.8407 (mm) cc_final: 0.8085 (mm) REVERT: A 115 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6911 (mtp180) REVERT: A 121 HIS cc_start: 0.7903 (m90) cc_final: 0.7523 (m90) REVERT: A 123 ASN cc_start: 0.6751 (m-40) cc_final: 0.6512 (m-40) REVERT: A 144 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7015 (mmmt) REVERT: A 158 HIS cc_start: 0.7781 (p-80) cc_final: 0.7557 (p-80) REVERT: A 171 ARG cc_start: 0.7518 (ttm110) cc_final: 0.6958 (ttm110) REVERT: A 215 GLU cc_start: 0.7720 (mp0) cc_final: 0.7075 (mp0) REVERT: B 66 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7161 (tp-100) REVERT: B 122 LYS cc_start: 0.8342 (tptt) cc_final: 0.7982 (tptt) REVERT: B 125 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 145 PHE cc_start: 0.7617 (t80) cc_final: 0.6975 (t80) REVERT: B 149 PHE cc_start: 0.7654 (m-80) cc_final: 0.7316 (m-80) REVERT: B 219 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6143 (t70) REVERT: B 244 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6781 (ttp-110) REVERT: B 248 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7556 (mtp85) REVERT: B 334 THR cc_start: 0.8271 (t) cc_final: 0.7958 (p) REVERT: B 336 ILE cc_start: 0.6803 (mm) cc_final: 0.6583 (tt) REVERT: B 338 GLU cc_start: 0.6940 (pp20) cc_final: 0.6690 (pp20) outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 0.2218 time to fit residues: 49.8805 Evaluate side-chains 187 residues out of total 571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.0020 chunk 61 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 HIS ** 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 = 0.4325 r_free = 0.4325 target = 0.155742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.131869 restraints weight = 10164.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.136123 restraints weight = 6125.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.138976 restraints weight = 4177.755| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 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 = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.6020 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= 0.196 Angle : 0.774 11.877 6974 Z= 0.378 Chirality : 0.049 0.233 790 Planarity : 0.006 0.051 881 Dihedral : 6.287 84.497 697 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.47 % Allowed : 29.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.33), residues: 621 helix: -0.55 (0.30), residues: 300 sheet: -3.75 (0.67), residues: 30 loop : -2.01 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.004 0.001 HIS A 121 PHE 0.014 0.001 PHE A 266 TYR 0.017 0.001 TYR B 55 ARG 0.007 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.29 seconds wall clock time: 50 minutes 9.67 seconds (3009.67 seconds total)