Starting phenix.real_space_refine on Sat Jul 26 21:25:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8trn_41584/07_2025/8trn_41584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8trn_41584/07_2025/8trn_41584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8trn_41584/07_2025/8trn_41584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8trn_41584/07_2025/8trn_41584.map" model { file = "/net/cci-nas-00/data/ceres_data/8trn_41584/07_2025/8trn_41584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8trn_41584/07_2025/8trn_41584.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.344 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 6 5.49 5 Mg 3 5.21 5 S 54 5.16 5 C 5580 2.51 5 N 1458 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8814 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2863 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, B Time building chain proxies: 6.83, per 1000 atoms: 0.77 Number of scatterers: 8814 At special positions: 0 Unit cell: (77.43, 99.68, 139.73, 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) Br 3 34.99 S 54 16.00 P 6 15.00 Mg 3 11.99 O 1710 8.00 N 1458 7.00 C 5580 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 18 sheets defined 49.9% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.562A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 113 through 127 removed outlier: 3.990A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.679A pdb=" N SER A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.520A pdb=" N LYS A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.669A pdb=" N GLU A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.041A pdb=" N TYR A 307 " --> pdb=" O THR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.512A pdb=" N SER A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.756A pdb=" N GLN A 355 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 367 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.603A pdb=" N VAL A 371 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.562A pdb=" N LYS B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.989A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.680A pdb=" N SER B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.521A pdb=" N LYS B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.668A pdb=" N GLU B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 303 through 307 removed outlier: 4.040A pdb=" N TYR B 307 " --> pdb=" O THR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.512A pdb=" N SER B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.757A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.603A pdb=" N VAL B 371 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.562A pdb=" N LYS C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 113 through 127 removed outlier: 3.989A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.679A pdb=" N SER C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 203 through 218 removed outlier: 3.520A pdb=" N LYS C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.668A pdb=" N GLU C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 290 through 296 Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.040A pdb=" N TYR C 307 " --> pdb=" O THR C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 338 through 350 removed outlier: 3.511A pdb=" N SER C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 350 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.757A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.603A pdb=" N VAL C 371 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.574A pdb=" N LEU A 9 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR A 107 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A 11 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 4.120A pdb=" N TYR A 54 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 171 removed outlier: 6.326A pdb=" N VAL A 298 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.574A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.120A pdb=" N TYR B 54 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.326A pdb=" N VAL B 298 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.573A pdb=" N LEU C 9 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR C 107 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL C 11 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55 removed outlier: 4.119A pdb=" N TYR C 54 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171 removed outlier: 6.327A pdb=" N VAL C 298 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 242 423 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 2841 1.34 - 1.48: 2205 1.48 - 1.62: 3864 1.62 - 1.75: 0 1.75 - 1.89: 99 Bond restraints: 9009 Sorted by residual: bond pdb=" N MET C 326 " pdb=" CA MET C 326 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.16e+00 bond pdb=" N MET A 326 " pdb=" CA MET A 326 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.27e-02 6.20e+03 7.02e+00 bond pdb=" N MET B 326 " pdb=" CA MET B 326 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.79e+00 bond pdb=" N GLU A 362 " pdb=" CA GLU A 362 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.39e+00 bond pdb=" N GLU B 362 " pdb=" CA GLU B 362 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.31e+00 ... (remaining 9004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 11759 1.70 - 3.40: 351 3.40 - 5.10: 73 5.10 - 6.80: 27 6.80 - 8.50: 18 Bond angle restraints: 12228 Sorted by residual: angle pdb=" CA MET B 326 " pdb=" C MET B 326 " pdb=" O MET B 326 " ideal model delta sigma weight residual 121.56 118.41 3.15 1.09e+00 8.42e-01 8.33e+00 angle pdb=" CA MET C 326 " pdb=" C MET C 326 " pdb=" O MET C 326 " ideal model delta sigma weight residual 121.56 118.42 3.14 1.09e+00 8.42e-01 8.29e+00 angle pdb=" CA MET A 326 " pdb=" C MET A 326 " pdb=" O MET A 326 " ideal model delta sigma weight residual 121.56 118.46 3.10 1.09e+00 8.42e-01 8.11e+00 angle pdb=" O 9UE B 403 " pdb=" C4 9UE B 403 " pdb=" C5 9UE B 403 " ideal model delta sigma weight residual 109.41 117.91 -8.50 3.00e+00 1.11e-01 8.02e+00 angle pdb=" O 9UE C 403 " pdb=" C4 9UE C 403 " pdb=" C5 9UE C 403 " ideal model delta sigma weight residual 109.41 117.91 -8.50 3.00e+00 1.11e-01 8.02e+00 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 5226 35.78 - 71.55: 156 71.55 - 107.33: 21 107.33 - 143.10: 42 143.10 - 178.88: 27 Dihedral angle restraints: 5472 sinusoidal: 2307 harmonic: 3165 Sorted by residual: dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 105.30 -165.30 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP C 402 " pdb=" O5' ADP C 402 " pdb=" PA ADP C 402 " pdb=" O2A ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 105.30 -165.29 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP A 402 " pdb=" O5' ADP A 402 " pdb=" PA ADP A 402 " pdb=" O2A ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 105.29 -165.28 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 5469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1309 0.117 - 0.234: 26 0.234 - 0.351: 10 0.351 - 0.468: 2 0.468 - 0.585: 3 Chirality restraints: 1350 Sorted by residual: chirality pdb=" C6 9UE A 403 " pdb=" N 9UE A 403 " pdb=" C29 9UE A 403 " pdb=" C5 9UE A 403 " both_signs ideal model delta sigma weight residual False -1.97 -2.56 0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" C6 9UE B 403 " pdb=" N 9UE B 403 " pdb=" C29 9UE B 403 " pdb=" C5 9UE B 403 " both_signs ideal model delta sigma weight residual False -1.97 -2.56 0.58 2.00e-01 2.50e+01 8.42e+00 chirality pdb=" C6 9UE C 403 " pdb=" N 9UE C 403 " pdb=" C29 9UE C 403 " pdb=" C5 9UE C 403 " both_signs ideal model delta sigma weight residual False -1.97 -2.55 0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1347 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 367 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 368 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 368 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 368 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 367 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 368 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 367 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO C 368 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 368 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 368 " 0.016 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 36 2.58 - 3.16: 6882 3.16 - 3.74: 12737 3.74 - 4.32: 19057 4.32 - 4.90: 32108 Nonbonded interactions: 70820 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O1B ADP C 402 " model vdw 1.995 2.170 nonbonded pdb="MG MG A 401 " pdb=" O1B ADP A 402 " model vdw 1.996 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1B ADP B 402 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP C 158 " pdb=" O3' ADP C 402 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP A 158 " pdb=" O3' ADP A 402 " model vdw 2.204 3.040 ... (remaining 70815 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.960 Find NCS groups from input model: 0.180 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:17.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9009 Z= 0.226 Angle : 0.808 8.498 12228 Z= 0.387 Chirality : 0.063 0.585 1350 Planarity : 0.004 0.030 1560 Dihedral : 26.112 178.877 3450 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.64 % Allowed : 13.10 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1095 helix: 0.03 (0.24), residues: 462 sheet: 0.51 (0.35), residues: 201 loop : 0.45 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 357 HIS 0.004 0.001 HIS C 162 PHE 0.010 0.002 PHE B 224 TYR 0.010 0.001 TYR C 295 ARG 0.004 0.001 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.20140 ( 417) hydrogen bonds : angle 6.66785 ( 1071) covalent geometry : bond 0.00482 ( 9009) covalent geometry : angle 0.80843 (12228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.920 Fit side-chains REVERT: A 70 TYR cc_start: 0.9069 (m-80) cc_final: 0.8739 (m-80) REVERT: A 168 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8406 (mt-10) REVERT: A 202 THR cc_start: 0.9017 (m) cc_final: 0.8762 (t) REVERT: A 208 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 327 LYS cc_start: 0.8277 (ptpt) cc_final: 0.7794 (mtmm) REVERT: B 13 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8085 (t0) REVERT: B 38 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8270 (mttp) REVERT: B 48 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7491 (ptt) REVERT: B 69 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8231 (mmmm) REVERT: B 327 LYS cc_start: 0.8025 (ptpt) cc_final: 0.7599 (mtmm) REVERT: B 356 MET cc_start: 0.8710 (mtm) cc_final: 0.8430 (mtt) REVERT: C 38 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8292 (mttp) REVERT: C 69 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7994 (mttm) REVERT: C 83 MET cc_start: 0.8981 (tpt) cc_final: 0.8619 (tpt) REVERT: C 97 VAL cc_start: 0.8981 (m) cc_final: 0.8766 (p) REVERT: C 134 TYR cc_start: 0.9083 (t80) cc_final: 0.8804 (t80) REVERT: C 289 ASP cc_start: 0.8459 (m-30) cc_final: 0.8223 (m-30) REVERT: C 327 LYS cc_start: 0.8006 (ptpt) cc_final: 0.7653 (mtmm) REVERT: C 364 ASP cc_start: 0.7905 (m-30) cc_final: 0.7666 (m-30) outliers start: 6 outliers final: 0 residues processed: 197 average time/residue: 1.5877 time to fit residues: 330.1289 Evaluate side-chains 160 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 48 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 74 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.091729 restraints weight = 9814.490| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.67 r_work: 0.2805 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9009 Z= 0.120 Angle : 0.601 7.826 12228 Z= 0.282 Chirality : 0.046 0.163 1350 Planarity : 0.004 0.032 1560 Dihedral : 32.544 179.977 1367 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.88 % Allowed : 16.93 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1095 helix: 0.71 (0.25), residues: 447 sheet: 0.59 (0.35), residues: 201 loop : 0.74 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 341 HIS 0.006 0.001 HIS A 74 PHE 0.011 0.001 PHE B 32 TYR 0.021 0.001 TYR A 295 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 417) hydrogen bonds : angle 4.75339 ( 1071) covalent geometry : bond 0.00267 ( 9009) covalent geometry : angle 0.60056 (12228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.8932 (m-80) cc_final: 0.8667 (m-80) REVERT: A 108 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: A 168 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8440 (mt-10) REVERT: A 202 THR cc_start: 0.8986 (m) cc_final: 0.8704 (t) REVERT: A 327 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7832 (mtmm) REVERT: B 38 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7830 (mtmt) REVERT: B 48 MET cc_start: 0.8196 (mmm) cc_final: 0.7458 (ptt) REVERT: B 67 THR cc_start: 0.8694 (t) cc_final: 0.8459 (p) REVERT: B 69 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8001 (mmmm) REVERT: B 96 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8177 (mtt-85) REVERT: B 238 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7816 (mm-30) REVERT: B 327 LYS cc_start: 0.8182 (ptpt) cc_final: 0.7727 (mtmm) REVERT: C 38 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7821 (mttp) REVERT: C 44 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7612 (tp) REVERT: C 69 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7759 (mttm) REVERT: C 83 MET cc_start: 0.8791 (tpt) cc_final: 0.8555 (tpt) REVERT: C 97 VAL cc_start: 0.8955 (m) cc_final: 0.8750 (p) REVERT: C 126 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7389 (mm-30) REVERT: C 289 ASP cc_start: 0.8497 (m-30) cc_final: 0.8281 (m-30) REVERT: C 327 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7704 (mtmm) REVERT: C 356 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8009 (mtm) outliers start: 27 outliers final: 10 residues processed: 167 average time/residue: 1.3444 time to fit residues: 237.9585 Evaluate side-chains 159 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN C 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.091317 restraints weight = 9563.032| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.65 r_work: 0.2802 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9009 Z= 0.125 Angle : 0.567 6.458 12228 Z= 0.264 Chirality : 0.046 0.163 1350 Planarity : 0.004 0.036 1560 Dihedral : 32.010 179.883 1364 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.30 % Allowed : 18.42 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.26), residues: 1095 helix: 1.17 (0.26), residues: 426 sheet: 0.87 (0.34), residues: 219 loop : 0.68 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.003 0.001 HIS A 74 PHE 0.010 0.001 PHE B 32 TYR 0.027 0.001 TYR A 295 ARG 0.004 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 417) hydrogen bonds : angle 4.46277 ( 1071) covalent geometry : bond 0.00298 ( 9009) covalent geometry : angle 0.56707 (12228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.8960 (m-80) cc_final: 0.8708 (m-80) REVERT: A 133 MET cc_start: 0.8818 (ptm) cc_final: 0.8562 (ptm) REVERT: A 134 TYR cc_start: 0.8908 (t80) cc_final: 0.8617 (t80) REVERT: A 148 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7221 (mtp180) REVERT: A 327 LYS cc_start: 0.8387 (ptpt) cc_final: 0.7894 (mtmm) REVERT: A 346 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8641 (mt) REVERT: B 38 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7802 (mtmt) REVERT: B 48 MET cc_start: 0.8206 (mmm) cc_final: 0.7429 (ptt) REVERT: B 69 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8013 (mmmm) REVERT: B 96 ARG cc_start: 0.8457 (ttm110) cc_final: 0.8178 (mtt-85) REVERT: B 238 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7899 (mm-30) REVERT: B 297 ASN cc_start: 0.8659 (t0) cc_final: 0.8455 (t0) REVERT: B 308 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: B 327 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7825 (mtmm) REVERT: C 38 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7731 (mtmm) REVERT: C 44 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7907 (tt) REVERT: C 69 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7742 (mttm) REVERT: C 73 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7182 (tt0) REVERT: C 126 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7329 (mm-30) REVERT: C 229 LYS cc_start: 0.7611 (tttt) cc_final: 0.7057 (ttmm) REVERT: C 327 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7755 (mtmm) REVERT: C 356 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8060 (mtm) outliers start: 31 outliers final: 10 residues processed: 169 average time/residue: 1.3860 time to fit residues: 247.7761 Evaluate side-chains 159 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.0060 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 297 ASN ** 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 = 0.3228 r_free = 0.3228 target = 0.114628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099653 restraints weight = 8567.370| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.52 r_work: 0.2866 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9009 Z= 0.081 Angle : 0.523 5.771 12228 Z= 0.240 Chirality : 0.044 0.198 1350 Planarity : 0.003 0.029 1560 Dihedral : 31.897 179.193 1362 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.56 % Allowed : 19.91 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.26), residues: 1095 helix: 1.42 (0.26), residues: 429 sheet: 0.70 (0.35), residues: 204 loop : 0.81 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 80 HIS 0.002 0.001 HIS C 74 PHE 0.008 0.001 PHE B 256 TYR 0.011 0.001 TYR A 295 ARG 0.005 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 417) hydrogen bonds : angle 4.28977 ( 1071) covalent geometry : bond 0.00171 ( 9009) covalent geometry : angle 0.52277 (12228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.920 Fit side-chains REVERT: A 134 TYR cc_start: 0.8881 (t80) cc_final: 0.8520 (t80) REVERT: A 148 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7141 (mtp180) REVERT: A 168 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8418 (mt-10) REVERT: A 208 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 327 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7906 (mtmm) REVERT: A 354 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8004 (mm-40) REVERT: B 38 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7657 (mtmm) REVERT: B 48 MET cc_start: 0.8233 (mmm) cc_final: 0.7571 (ptt) REVERT: B 69 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8015 (mmmm) REVERT: B 96 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8163 (mtt-85) REVERT: B 133 MET cc_start: 0.8873 (ptm) cc_final: 0.8666 (ttp) REVERT: B 148 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: B 238 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7871 (mm-30) REVERT: B 297 ASN cc_start: 0.8442 (t0) cc_final: 0.8195 (t0) REVERT: B 327 LYS cc_start: 0.8236 (ptpt) cc_final: 0.7805 (mtmm) REVERT: B 365 GLU cc_start: 0.7697 (tp30) cc_final: 0.7394 (tp30) REVERT: C 44 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7636 (tp) REVERT: C 65 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8793 (pp) REVERT: C 69 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7731 (mttm) REVERT: C 73 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: C 126 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7237 (mm-30) REVERT: C 229 LYS cc_start: 0.7563 (tttt) cc_final: 0.7003 (ttmm) REVERT: C 327 LYS cc_start: 0.8160 (ptpt) cc_final: 0.7732 (mtmm) REVERT: C 356 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8034 (mtm) outliers start: 24 outliers final: 9 residues processed: 170 average time/residue: 1.3914 time to fit residues: 249.8774 Evaluate side-chains 161 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.091114 restraints weight = 8784.748| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.62 r_work: 0.2790 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9009 Z= 0.163 Angle : 0.582 6.091 12228 Z= 0.272 Chirality : 0.047 0.203 1350 Planarity : 0.004 0.035 1560 Dihedral : 31.642 179.601 1362 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.73 % Allowed : 19.38 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.25), residues: 1095 helix: 1.37 (0.25), residues: 426 sheet: 0.79 (0.34), residues: 219 loop : 0.69 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 341 HIS 0.004 0.001 HIS A 162 PHE 0.010 0.001 PHE B 32 TYR 0.015 0.001 TYR A 295 ARG 0.005 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 417) hydrogen bonds : angle 4.43149 ( 1071) covalent geometry : bond 0.00406 ( 9009) covalent geometry : angle 0.58237 (12228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.934 Fit side-chains REVERT: A 108 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: A 134 TYR cc_start: 0.8999 (t80) cc_final: 0.8648 (t80) REVERT: A 148 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7141 (mtp180) REVERT: A 168 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8415 (mt-10) REVERT: A 208 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 327 LYS cc_start: 0.8475 (ptpt) cc_final: 0.7972 (mtmm) REVERT: A 346 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8664 (mt) REVERT: A 354 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8106 (mm-40) REVERT: B 29 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7681 (ptp-170) REVERT: B 38 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7808 (mtmm) REVERT: B 48 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7533 (ptt) REVERT: B 69 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8017 (mmmm) REVERT: B 96 ARG cc_start: 0.8408 (ttm110) cc_final: 0.8176 (mtt-85) REVERT: B 226 GLU cc_start: 0.7933 (tp30) cc_final: 0.7649 (mm-30) REVERT: B 327 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7805 (mtmm) REVERT: B 352 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8042 (p) REVERT: B 365 GLU cc_start: 0.7739 (tp30) cc_final: 0.7445 (tp30) REVERT: C 44 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7987 (tt) REVERT: C 65 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8826 (pp) REVERT: C 69 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7712 (mttm) REVERT: C 73 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: C 114 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7849 (mttm) REVERT: C 126 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7348 (mm-30) REVERT: C 229 LYS cc_start: 0.7656 (tttt) cc_final: 0.7101 (ttmm) REVERT: C 242 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: C 327 LYS cc_start: 0.8250 (ptpt) cc_final: 0.7825 (mtmm) REVERT: C 356 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8113 (mtm) outliers start: 35 outliers final: 15 residues processed: 166 average time/residue: 1.4200 time to fit residues: 248.7980 Evaluate side-chains 168 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 297 ASN ** 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 = 0.3132 r_free = 0.3132 target = 0.107948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.092420 restraints weight = 8782.909| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.61 r_work: 0.2800 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9009 Z= 0.139 Angle : 0.563 6.096 12228 Z= 0.261 Chirality : 0.046 0.205 1350 Planarity : 0.004 0.031 1560 Dihedral : 31.403 179.684 1362 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.73 % Allowed : 19.17 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.26), residues: 1095 helix: 1.42 (0.25), residues: 423 sheet: 0.79 (0.34), residues: 219 loop : 0.69 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 87 HIS 0.004 0.001 HIS B 162 PHE 0.009 0.001 PHE A 32 TYR 0.012 0.001 TYR A 295 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 417) hydrogen bonds : angle 4.39976 ( 1071) covalent geometry : bond 0.00340 ( 9009) covalent geometry : angle 0.56313 (12228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.054 Fit side-chains REVERT: A 73 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: A 108 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: A 134 TYR cc_start: 0.8971 (t80) cc_final: 0.8649 (t80) REVERT: A 148 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7215 (mtp180) REVERT: A 168 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8426 (mt-10) REVERT: A 208 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 297 ASN cc_start: 0.8265 (t0) cc_final: 0.7389 (t0) REVERT: A 327 LYS cc_start: 0.8482 (ptpt) cc_final: 0.7982 (mtmm) REVERT: A 346 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8655 (mt) REVERT: A 354 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8062 (mm-40) REVERT: B 29 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7698 (ptp-170) REVERT: B 38 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7795 (mtmm) REVERT: B 48 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7543 (ptt) REVERT: B 69 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8043 (mmmm) REVERT: B 96 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8185 (mtt-85) REVERT: B 226 GLU cc_start: 0.7941 (tp30) cc_final: 0.7664 (mm-30) REVERT: B 238 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7813 (mm-30) REVERT: B 327 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7825 (mtmm) REVERT: B 352 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 365 GLU cc_start: 0.7766 (tp30) cc_final: 0.7470 (tp30) REVERT: C 44 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7949 (tt) REVERT: C 65 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8832 (pp) REVERT: C 69 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7704 (mttm) REVERT: C 73 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: C 126 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 229 LYS cc_start: 0.7703 (tttt) cc_final: 0.7146 (ttmm) REVERT: C 327 LYS cc_start: 0.8331 (ptpt) cc_final: 0.7882 (mtmm) REVERT: C 356 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8163 (mtm) outliers start: 35 outliers final: 17 residues processed: 164 average time/residue: 1.4731 time to fit residues: 255.1249 Evaluate side-chains 176 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 162 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.093202 restraints weight = 8819.573| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.61 r_work: 0.2795 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9009 Z= 0.138 Angle : 0.562 6.041 12228 Z= 0.261 Chirality : 0.046 0.213 1350 Planarity : 0.004 0.033 1560 Dihedral : 30.973 173.541 1362 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.47 % Allowed : 18.42 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.26), residues: 1095 helix: 1.46 (0.25), residues: 423 sheet: 0.81 (0.34), residues: 219 loop : 0.71 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 87 HIS 0.004 0.001 HIS B 74 PHE 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR A 295 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 417) hydrogen bonds : angle 4.38636 ( 1071) covalent geometry : bond 0.00339 ( 9009) covalent geometry : angle 0.56192 (12228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.955 Fit side-chains REVERT: A 38 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7903 (mppt) REVERT: A 73 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: A 108 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: A 134 TYR cc_start: 0.8953 (t80) cc_final: 0.8630 (t80) REVERT: A 168 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8403 (mt-10) REVERT: A 208 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 271 GLU cc_start: 0.8199 (tt0) cc_final: 0.7902 (tt0) REVERT: A 297 ASN cc_start: 0.8393 (t0) cc_final: 0.7901 (t0) REVERT: A 327 LYS cc_start: 0.8485 (ptpt) cc_final: 0.7981 (mtmm) REVERT: A 346 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8665 (mt) REVERT: A 354 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7865 (mm-40) REVERT: B 29 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7694 (ptp-170) REVERT: B 38 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7829 (mtmm) REVERT: B 48 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7521 (ptt) REVERT: B 69 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (mmmm) REVERT: B 108 GLU cc_start: 0.8724 (tt0) cc_final: 0.8504 (tt0) REVERT: B 226 GLU cc_start: 0.7958 (tp30) cc_final: 0.7693 (mm-30) REVERT: B 238 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7807 (mm-30) REVERT: B 308 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: B 320 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 327 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7830 (mtmm) REVERT: B 352 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8086 (p) REVERT: B 365 GLU cc_start: 0.7778 (tp30) cc_final: 0.7473 (tp30) REVERT: C 7 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: C 44 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7983 (tt) REVERT: C 65 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8797 (pp) REVERT: C 69 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7708 (mttm) REVERT: C 73 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: C 126 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7356 (mm-30) REVERT: C 229 LYS cc_start: 0.7692 (tttt) cc_final: 0.7192 (ttmt) REVERT: C 327 LYS cc_start: 0.8327 (ptpt) cc_final: 0.7882 (mtmm) outliers start: 42 outliers final: 18 residues processed: 168 average time/residue: 1.4524 time to fit residues: 257.5867 Evaluate side-chains 178 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 48 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** 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 = 0.3137 r_free = 0.3137 target = 0.108700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093908 restraints weight = 9198.878| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.52 r_work: 0.2839 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9009 Z= 0.092 Angle : 0.534 5.896 12228 Z= 0.246 Chirality : 0.045 0.217 1350 Planarity : 0.004 0.036 1560 Dihedral : 30.529 172.365 1362 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.62 % Allowed : 19.49 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.26), residues: 1095 helix: 1.64 (0.26), residues: 423 sheet: 0.84 (0.35), residues: 219 loop : 0.82 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 87 HIS 0.005 0.001 HIS B 74 PHE 0.008 0.001 PHE B 256 TYR 0.011 0.001 TYR A 295 ARG 0.008 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 417) hydrogen bonds : angle 4.28973 ( 1071) covalent geometry : bond 0.00212 ( 9009) covalent geometry : angle 0.53434 (12228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.916 Fit side-chains REVERT: A 38 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7833 (mppt) REVERT: A 108 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: A 134 TYR cc_start: 0.8830 (t80) cc_final: 0.8478 (t80) REVERT: A 168 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8390 (mt-10) REVERT: A 208 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 271 GLU cc_start: 0.8204 (tt0) cc_final: 0.7914 (tt0) REVERT: A 327 LYS cc_start: 0.8451 (ptpt) cc_final: 0.7942 (mtmm) REVERT: A 354 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7827 (mm-40) REVERT: B 38 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7657 (mppt) REVERT: B 48 MET cc_start: 0.8256 (mmm) cc_final: 0.7622 (ptt) REVERT: B 69 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8036 (mmmm) REVERT: B 108 GLU cc_start: 0.8699 (tt0) cc_final: 0.8479 (tt0) REVERT: B 226 GLU cc_start: 0.7915 (tp30) cc_final: 0.7662 (mm-30) REVERT: B 238 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7812 (mm-30) REVERT: B 327 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7751 (mtmm) REVERT: B 365 GLU cc_start: 0.7756 (tp30) cc_final: 0.7448 (tp30) REVERT: C 44 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7730 (tp) REVERT: C 45 MET cc_start: 0.8488 (mmm) cc_final: 0.8186 (mmm) REVERT: C 65 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8699 (pp) REVERT: C 69 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7677 (mttm) REVERT: C 73 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: C 126 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7278 (mm-30) REVERT: C 229 LYS cc_start: 0.7622 (tttt) cc_final: 0.7128 (ttmt) REVERT: C 327 LYS cc_start: 0.8315 (ptpt) cc_final: 0.7865 (mtmm) REVERT: C 356 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8114 (mtm) outliers start: 34 outliers final: 15 residues processed: 165 average time/residue: 1.5271 time to fit residues: 266.3782 Evaluate side-chains 169 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.093011 restraints weight = 9124.112| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.52 r_work: 0.2829 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9009 Z= 0.114 Angle : 0.548 7.995 12228 Z= 0.251 Chirality : 0.046 0.211 1350 Planarity : 0.004 0.033 1560 Dihedral : 30.294 171.607 1362 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.73 % Allowed : 19.38 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.26), residues: 1095 helix: 1.65 (0.26), residues: 423 sheet: 0.86 (0.35), residues: 219 loop : 0.80 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.006 0.001 HIS B 74 PHE 0.008 0.001 PHE A 32 TYR 0.010 0.001 TYR A 295 ARG 0.008 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 417) hydrogen bonds : angle 4.30353 ( 1071) covalent geometry : bond 0.00275 ( 9009) covalent geometry : angle 0.54825 (12228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.924 Fit side-chains REVERT: A 38 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7850 (mppt) REVERT: A 70 TYR cc_start: 0.8928 (m-80) cc_final: 0.8683 (m-80) REVERT: A 108 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 134 TYR cc_start: 0.8833 (t80) cc_final: 0.8548 (t80) REVERT: A 168 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8354 (mt-10) REVERT: A 208 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7227 (mm-30) REVERT: A 327 LYS cc_start: 0.8453 (ptpt) cc_final: 0.7942 (mtmm) REVERT: A 354 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7827 (mm-40) REVERT: B 38 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7537 (mppt) REVERT: B 48 MET cc_start: 0.8240 (mmm) cc_final: 0.7610 (ptt) REVERT: B 69 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8032 (mmmm) REVERT: B 108 GLU cc_start: 0.8703 (tt0) cc_final: 0.8483 (tt0) REVERT: B 226 GLU cc_start: 0.7892 (tp30) cc_final: 0.7632 (mm-30) REVERT: B 238 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7842 (mm-30) REVERT: B 308 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: B 320 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 327 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7737 (mtmm) REVERT: B 352 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 365 GLU cc_start: 0.7742 (tp30) cc_final: 0.7441 (tp30) REVERT: C 44 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7934 (tt) REVERT: C 45 MET cc_start: 0.8485 (mmm) cc_final: 0.8181 (mmm) REVERT: C 65 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8708 (pp) REVERT: C 69 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7656 (mttm) REVERT: C 73 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: C 126 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7269 (mm-30) REVERT: C 229 LYS cc_start: 0.7607 (tttt) cc_final: 0.7116 (ttmt) REVERT: C 327 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7856 (mtmm) REVERT: C 356 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8127 (mtm) outliers start: 35 outliers final: 19 residues processed: 165 average time/residue: 1.3756 time to fit residues: 240.0466 Evaluate side-chains 176 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** 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 = 0.3128 r_free = 0.3128 target = 0.108113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.092789 restraints weight = 9576.189| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.65 r_work: 0.2827 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9009 Z= 0.104 Angle : 0.547 8.023 12228 Z= 0.251 Chirality : 0.045 0.209 1350 Planarity : 0.004 0.033 1560 Dihedral : 30.069 172.005 1362 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.30 % Allowed : 19.60 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.26), residues: 1095 helix: 1.70 (0.26), residues: 420 sheet: 0.88 (0.35), residues: 219 loop : 0.82 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 87 HIS 0.007 0.001 HIS B 74 PHE 0.008 0.001 PHE A 32 TYR 0.010 0.001 TYR A 295 ARG 0.009 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 417) hydrogen bonds : angle 4.28781 ( 1071) covalent geometry : bond 0.00245 ( 9009) covalent geometry : angle 0.54708 (12228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.005 Fit side-chains REVERT: A 38 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7912 (mppt) REVERT: A 108 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: A 134 TYR cc_start: 0.8858 (t80) cc_final: 0.8580 (t80) REVERT: A 168 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8419 (mt-10) REVERT: A 208 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 327 LYS cc_start: 0.8453 (ptpt) cc_final: 0.7941 (mtmm) REVERT: A 354 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7853 (mm-40) REVERT: B 38 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7597 (mppt) REVERT: B 48 MET cc_start: 0.8276 (mmm) cc_final: 0.7626 (ptt) REVERT: B 69 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8084 (mmmm) REVERT: B 148 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7515 (ttp-170) REVERT: B 226 GLU cc_start: 0.7960 (tp30) cc_final: 0.7723 (mm-30) REVERT: B 238 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7868 (mm-30) REVERT: B 308 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: B 327 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7757 (mtmm) REVERT: B 352 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8087 (p) REVERT: C 44 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7961 (tt) REVERT: C 65 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8753 (pp) REVERT: C 69 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7736 (mttm) REVERT: C 73 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: C 126 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7281 (mm-30) REVERT: C 229 LYS cc_start: 0.7630 (tttt) cc_final: 0.7157 (ttmt) REVERT: C 327 LYS cc_start: 0.8327 (ptpt) cc_final: 0.7892 (mtmm) REVERT: C 356 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8123 (mtm) REVERT: C 364 ASP cc_start: 0.7998 (m-30) cc_final: 0.7676 (m-30) outliers start: 31 outliers final: 20 residues processed: 156 average time/residue: 1.4654 time to fit residues: 241.5039 Evaluate side-chains 171 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 297 ASN ** 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 = 0.3121 r_free = 0.3121 target = 0.107653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.092386 restraints weight = 9463.689| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.64 r_work: 0.2814 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9009 Z= 0.116 Angle : 0.555 8.060 12228 Z= 0.254 Chirality : 0.046 0.212 1350 Planarity : 0.004 0.032 1560 Dihedral : 29.951 172.237 1362 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.41 % Allowed : 19.81 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.26), residues: 1095 helix: 1.69 (0.26), residues: 420 sheet: 0.88 (0.35), residues: 219 loop : 0.82 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 87 HIS 0.008 0.001 HIS B 74 PHE 0.008 0.001 PHE A 32 TYR 0.009 0.001 TYR A 295 ARG 0.009 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 417) hydrogen bonds : angle 4.29546 ( 1071) covalent geometry : bond 0.00281 ( 9009) covalent geometry : angle 0.55467 (12228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6629.78 seconds wall clock time: 114 minutes 28.58 seconds (6868.58 seconds total)