Starting phenix.real_space_refine on Thu Jul 2 13:12:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jv5_22493/07_2026/7jv5_22493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jv5_22493/07_2026/7jv5_22493.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/7jv5_22493/07_2026/7jv5_22493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jv5_22493/07_2026/7jv5_22493.map" model { file = "/net/cci-nas-00/data/ceres_data/7jv5_22493/07_2026/7jv5_22493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jv5_22493/07_2026/7jv5_22493.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jv5_22493/07_2026/7jv5_22493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jv5_22493/07_2026/7jv5_22493.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 Cl 1 4.86 5 C 5493 2.51 5 N 1444 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8531 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2244 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 3 Chain: "A" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1978 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2604 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 296 Unusual residues: {'CLR': 6, 'PLM': 6, 'SK0': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Time building chain proxies: 1.53, per 1000 atoms: 0.18 Number of scatterers: 8531 At special positions: 0 Unit cell: (106.47, 98.358, 120.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 54 16.00 O 1539 8.00 N 1444 7.00 C 5493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 290.8 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 44.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'R' and resid 21 through 51 Processing helix chain 'R' and resid 52 through 57 removed outlier: 3.826A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.148A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.477A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 135 Processing helix chain 'R' and resid 136 through 156 Processing helix chain 'R' and resid 157 through 162 Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 240 Processing helix chain 'R' and resid 264 through 295 removed outlier: 3.998A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 296 through 298 No H-bonds generated for 'chain 'R' and resid 296 through 298' Processing helix chain 'R' and resid 309 through 332 removed outlier: 4.580A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.595A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 4.055A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.219A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.948A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.554A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.191A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.736A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.979A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.600A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.599A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.157A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.904A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.773A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.681A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.780A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.590A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2419 1.34 - 1.46: 1815 1.46 - 1.58: 4404 1.58 - 1.70: 0 1.70 - 1.83: 74 Bond restraints: 8712 Sorted by residual: bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.76e+00 bond pdb=" C ILE R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.59e+00 bond pdb=" CA PHE R 297 " pdb=" C PHE R 297 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.80e-02 3.09e+03 3.42e+00 bond pdb=" C LEU R 295 " pdb=" N PRO R 296 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.35e+00 bond pdb=" C ASN R 327 " pdb=" N PRO R 328 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 ... (remaining 8707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 10959 2.05 - 4.09: 742 4.09 - 6.14: 71 6.14 - 8.18: 19 8.18 - 10.23: 5 Bond angle restraints: 11796 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" N MET R 78 " pdb=" CA MET R 78 " pdb=" C MET R 78 " ideal model delta sigma weight residual 109.81 119.30 -9.49 2.21e+00 2.05e-01 1.84e+01 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 111.11 116.04 -4.93 1.20e+00 6.94e-01 1.69e+01 angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 110.62 115.17 -4.55 1.14e+00 7.69e-01 1.59e+01 angle pdb=" N LYS A 17 " pdb=" CA LYS A 17 " pdb=" C LYS A 17 " ideal model delta sigma weight residual 111.37 117.33 -5.96 1.65e+00 3.67e-01 1.31e+01 ... (remaining 11791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 4864 15.04 - 30.07: 258 30.07 - 45.11: 34 45.11 - 60.15: 2 60.15 - 75.18: 2 Dihedral angle restraints: 5160 sinusoidal: 2118 harmonic: 3042 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 153.14 26.86 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA SER N 49 " pdb=" C SER N 49 " pdb=" N ASP N 50 " pdb=" CA ASP N 50 " ideal model delta harmonic sigma weight residual 180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA LEU B 198 " pdb=" C LEU B 198 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1127 0.085 - 0.170: 169 0.170 - 0.254: 24 0.254 - 0.339: 7 0.339 - 0.424: 7 Chirality restraints: 1334 Sorted by residual: chirality pdb=" C14 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C15 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 1331 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 207 " 0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C VAL R 207 " -0.074 2.00e-02 2.50e+03 pdb=" O VAL R 207 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 208 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 218 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C TYR R 218 " 0.073 2.00e-02 2.50e+03 pdb=" O TYR R 218 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG R 219 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 272 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C LYS R 272 " -0.072 2.00e-02 2.50e+03 pdb=" O LYS R 272 " 0.027 2.00e-02 2.50e+03 pdb=" N THR R 273 " 0.025 2.00e-02 2.50e+03 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1224 2.77 - 3.30: 7752 3.30 - 3.84: 13286 3.84 - 4.37: 15683 4.37 - 4.90: 27429 Nonbonded interactions: 65374 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.276 3.040 nonbonded pdb=" O TRP N 47 " pdb=" OG1 THR N 61 " model vdw 2.329 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.339 3.040 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.345 3.120 ... (remaining 65369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.820 Find NCS groups from input model: 0.040 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:5.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 0.051 8716 Z= 0.263 Angle : 1.087 10.230 11804 Z= 0.624 Chirality : 0.070 0.424 1334 Planarity : 0.009 0.076 1453 Dihedral : 9.281 75.182 3172 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.22), residues: 1024 helix: -2.90 (0.18), residues: 413 sheet: -0.01 (0.33), residues: 232 loop : -2.01 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 385 TYR 0.020 0.002 TYR R 331 PHE 0.040 0.003 PHE B 234 TRP 0.023 0.003 TRP N 36 HIS 0.010 0.003 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.26 ( 8712) covalent geometry : angle 1.08720 / 0.62 (11796) SS BOND : bond 0.00304 / 0.15 ( 4) SS BOND : angle 1.23926 / 0.72 ( 8) hydrogen bonds : bond 0.13551 / 9.02 ( 452) hydrogen bonds : angle 7.02221 / 4.93 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7224 (mmmt) cc_final: 0.5561 (tttm) REVERT: A 317 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8225 (ptt-90) REVERT: A 392 GLU cc_start: 0.8387 (tt0) cc_final: 0.7943 (tp30) REVERT: B 46 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7486 (mtp-110) REVERT: B 134 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6768 (pmt170) REVERT: B 163 ASP cc_start: 0.8713 (p0) cc_final: 0.8502 (p0) REVERT: B 175 GLN cc_start: 0.8563 (mt0) cc_final: 0.7951 (mm-40) REVERT: B 217 MET cc_start: 0.8622 (ptt) cc_final: 0.8300 (ppp) REVERT: B 226 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8540 (mt-10) REVERT: B 239 ASN cc_start: 0.8036 (m-40) cc_final: 0.7240 (t0) REVERT: B 303 ASP cc_start: 0.7805 (t0) cc_final: 0.7472 (p0) REVERT: B 315 VAL cc_start: 0.8675 (t) cc_final: 0.8259 (p) REVERT: G 21 MET cc_start: 0.8095 (mtt) cc_final: 0.7405 (tmm) REVERT: G 61 PHE cc_start: 0.8183 (m-80) cc_final: 0.7903 (m-80) REVERT: N 53 GLN cc_start: 0.8493 (mp10) cc_final: 0.8293 (mp10) REVERT: N 72 ARG cc_start: 0.8322 (ptm160) cc_final: 0.8062 (ppp80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.4840 time to fit residues: 96.4790 Evaluate side-chains 106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 262 GLN A 387 HIS B 142 HIS B 176 GLN B 266 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.181828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134692 restraints weight = 9505.219| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.22 r_work: 0.3712 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8716 Z= 0.171 Angle : 0.602 6.885 11804 Z= 0.318 Chirality : 0.043 0.165 1334 Planarity : 0.005 0.047 1453 Dihedral : 6.478 58.258 1274 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.90 % Allowed : 10.14 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1024 helix: 0.50 (0.23), residues: 422 sheet: 0.38 (0.34), residues: 226 loop : -1.33 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 27 TYR 0.014 0.002 TYR B 105 PHE 0.016 0.002 PHE R 333 TRP 0.019 0.002 TRP B 82 HIS 0.006 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8712) covalent geometry : angle 0.60145 / 0.32 (11796) SS BOND : bond 0.00255 / 0.13 ( 4) SS BOND : angle 0.98114 / 0.58 ( 8) hydrogen bonds : bond 0.05118 / 3.41 ( 452) hydrogen bonds : angle 4.98243 / 3.46 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 227 ARG cc_start: 0.6757 (mtm-85) cc_final: 0.6404 (mtp180) REVERT: A 221 MET cc_start: 0.7764 (ttm) cc_final: 0.7506 (ttt) REVERT: A 229 ASP cc_start: 0.7856 (t0) cc_final: 0.7299 (p0) REVERT: A 307 LYS cc_start: 0.6660 (mmmt) cc_final: 0.5390 (tttm) REVERT: A 314 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6829 (pm20) REVERT: A 317 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7830 (ptt-90) REVERT: A 343 ASP cc_start: 0.7782 (m-30) cc_final: 0.7568 (m-30) REVERT: A 392 GLU cc_start: 0.7871 (tt0) cc_final: 0.7187 (tp30) REVERT: B 46 ARG cc_start: 0.6683 (ttm-80) cc_final: 0.6118 (mtp85) REVERT: B 68 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6992 (mmm-85) REVERT: B 75 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: B 134 ARG cc_start: 0.6375 (mtm-85) cc_final: 0.5816 (pmt170) REVERT: B 138 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8330 (mm-30) REVERT: B 175 GLN cc_start: 0.7574 (mt0) cc_final: 0.6896 (mm-40) REVERT: B 189 SER cc_start: 0.8398 (p) cc_final: 0.8193 (m) REVERT: B 205 ASP cc_start: 0.6836 (p0) cc_final: 0.6497 (p0) REVERT: B 212 ASP cc_start: 0.6663 (t0) cc_final: 0.6283 (t0) REVERT: B 214 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8428 (tpp80) REVERT: B 217 MET cc_start: 0.7683 (ptt) cc_final: 0.7174 (ppp) REVERT: B 226 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7627 (mt-10) REVERT: B 239 ASN cc_start: 0.7091 (m-40) cc_final: 0.6581 (t0) REVERT: B 254 ASP cc_start: 0.7658 (t0) cc_final: 0.7344 (t0) REVERT: B 277 SER cc_start: 0.9022 (t) cc_final: 0.8778 (p) REVERT: B 298 ASP cc_start: 0.7298 (t0) cc_final: 0.6873 (t70) REVERT: B 303 ASP cc_start: 0.6702 (t0) cc_final: 0.6216 (p0) REVERT: B 315 VAL cc_start: 0.8451 (t) cc_final: 0.8207 (p) REVERT: G 21 MET cc_start: 0.7481 (mtt) cc_final: 0.6917 (tmm) REVERT: N 53 GLN cc_start: 0.7619 (mp10) cc_final: 0.7345 (mp10) outliers start: 26 outliers final: 11 residues processed: 152 average time/residue: 0.4500 time to fit residues: 72.8899 Evaluate side-chains 125 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.181251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.133728 restraints weight = 9356.248| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.25 r_work: 0.3656 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8716 Z= 0.118 Angle : 0.516 6.466 11804 Z= 0.269 Chirality : 0.041 0.162 1334 Planarity : 0.004 0.043 1453 Dihedral : 6.233 59.455 1274 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.01 % Allowed : 12.15 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1024 helix: 2.05 (0.25), residues: 428 sheet: 0.38 (0.34), residues: 224 loop : -1.15 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.010 0.001 TYR B 59 PHE 0.013 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8712) covalent geometry : angle 0.51595 / 0.27 (11796) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.85216 / 0.52 ( 8) hydrogen bonds : bond 0.04511 / 3.00 ( 452) hydrogen bonds : angle 4.55206 / 3.17 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.7850 (ttm) cc_final: 0.7576 (ttp) REVERT: A 229 ASP cc_start: 0.7985 (t0) cc_final: 0.7734 (t70) REVERT: A 314 GLU cc_start: 0.7876 (mt-10) cc_final: 0.6984 (pm20) REVERT: A 317 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7968 (ptt-90) REVERT: A 392 GLU cc_start: 0.7971 (tt0) cc_final: 0.7415 (tp30) REVERT: B 68 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7127 (mmm-85) REVERT: B 134 ARG cc_start: 0.6495 (mtm-85) cc_final: 0.5830 (pmt170) REVERT: B 175 GLN cc_start: 0.7581 (mt0) cc_final: 0.6971 (mm-40) REVERT: B 189 SER cc_start: 0.8441 (p) cc_final: 0.8171 (m) REVERT: B 205 ASP cc_start: 0.7088 (p0) cc_final: 0.6707 (p0) REVERT: B 212 ASP cc_start: 0.6781 (t0) cc_final: 0.6485 (t0) REVERT: B 217 MET cc_start: 0.7844 (ptt) cc_final: 0.7407 (ppp) REVERT: B 226 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 239 ASN cc_start: 0.7108 (m-40) cc_final: 0.6321 (t0) REVERT: B 254 ASP cc_start: 0.7697 (t0) cc_final: 0.7421 (t0) REVERT: B 277 SER cc_start: 0.9069 (t) cc_final: 0.8866 (p) REVERT: B 303 ASP cc_start: 0.6630 (t0) cc_final: 0.6213 (p0) REVERT: G 21 MET cc_start: 0.7424 (mtt) cc_final: 0.6898 (tmm) REVERT: N 53 GLN cc_start: 0.7743 (mp10) cc_final: 0.7374 (mp10) outliers start: 27 outliers final: 12 residues processed: 130 average time/residue: 0.4247 time to fit residues: 59.0271 Evaluate side-chains 109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.133676 restraints weight = 9563.733| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.20 r_work: 0.3628 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8716 Z= 0.121 Angle : 0.505 6.332 11804 Z= 0.263 Chirality : 0.041 0.153 1334 Planarity : 0.004 0.046 1453 Dihedral : 6.178 59.949 1274 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.90 % Allowed : 13.49 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 1024 helix: 2.38 (0.25), residues: 434 sheet: 0.23 (0.34), residues: 231 loop : -1.02 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 27 TYR 0.008 0.001 TYR A 339 PHE 0.014 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8712) covalent geometry : angle 0.50431 / 0.26 (11796) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 0.81315 / 0.50 ( 8) hydrogen bonds : bond 0.04370 / 2.90 ( 452) hydrogen bonds : angle 4.44499 / 3.09 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.286 Fit side-chains REVERT: R 132 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 60 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6673 (mpt) REVERT: A 221 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7609 (mtp) REVERT: A 229 ASP cc_start: 0.8127 (t0) cc_final: 0.7614 (t0) REVERT: A 314 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 317 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.8021 (ptt90) REVERT: A 392 GLU cc_start: 0.8099 (tt0) cc_final: 0.7407 (tp30) REVERT: B 68 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7153 (mmm-85) REVERT: B 134 ARG cc_start: 0.6606 (mtm-85) cc_final: 0.5774 (pmt170) REVERT: B 138 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8053 (mm-30) REVERT: B 175 GLN cc_start: 0.7840 (mt0) cc_final: 0.7160 (mm110) REVERT: B 180 PHE cc_start: 0.4379 (OUTLIER) cc_final: 0.1993 (p90) REVERT: B 189 SER cc_start: 0.8462 (p) cc_final: 0.8226 (m) REVERT: B 205 ASP cc_start: 0.7087 (p0) cc_final: 0.6711 (p0) REVERT: B 212 ASP cc_start: 0.6788 (t0) cc_final: 0.6513 (t0) REVERT: B 214 ARG cc_start: 0.8870 (tpp80) cc_final: 0.8519 (tpp80) REVERT: B 217 MET cc_start: 0.7838 (ptt) cc_final: 0.7443 (ppp) REVERT: B 226 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 239 ASN cc_start: 0.7225 (m-40) cc_final: 0.6793 (t0) REVERT: B 254 ASP cc_start: 0.7772 (t0) cc_final: 0.7518 (t0) REVERT: B 298 ASP cc_start: 0.7927 (t70) cc_final: 0.7566 (t70) REVERT: B 303 ASP cc_start: 0.6755 (t0) cc_final: 0.6299 (p0) REVERT: B 339 TRP cc_start: 0.8594 (m100) cc_final: 0.8070 (m-10) REVERT: G 21 MET cc_start: 0.7273 (mtt) cc_final: 0.6790 (tmm) REVERT: N 53 GLN cc_start: 0.7737 (mp10) cc_final: 0.7275 (mp10) REVERT: N 98 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7680 (ttt-90) REVERT: N 105 ARG cc_start: 0.7215 (mtm180) cc_final: 0.6734 (mtm180) outliers start: 26 outliers final: 12 residues processed: 119 average time/residue: 0.4384 time to fit residues: 55.7223 Evaluate side-chains 108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 41 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.177931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130973 restraints weight = 9632.522| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.21 r_work: 0.3644 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8716 Z= 0.128 Angle : 0.511 7.261 11804 Z= 0.265 Chirality : 0.041 0.151 1334 Planarity : 0.004 0.047 1453 Dihedral : 6.174 58.679 1274 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.01 % Allowed : 13.71 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.27), residues: 1024 helix: 2.55 (0.25), residues: 430 sheet: 0.15 (0.33), residues: 234 loop : -1.04 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.010 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8712) covalent geometry : angle 0.51070 / 0.26 (11796) SS BOND : bond 0.00105 / 0.05 ( 4) SS BOND : angle 0.86726 / 0.54 ( 8) hydrogen bonds : bond 0.04407 / 2.92 ( 452) hydrogen bonds : angle 4.40731 / 3.07 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: R 132 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 60 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6335 (mpt) REVERT: A 221 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7501 (mtp) REVERT: A 229 ASP cc_start: 0.8041 (t0) cc_final: 0.7548 (t0) REVERT: A 314 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7200 (pm20) REVERT: A 317 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.8008 (ptt-90) REVERT: A 392 GLU cc_start: 0.7972 (tt0) cc_final: 0.7270 (tp30) REVERT: B 46 ARG cc_start: 0.6784 (ttm-80) cc_final: 0.6209 (mtp-110) REVERT: B 58 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7775 (mm) REVERT: B 68 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.7028 (mmm-85) REVERT: B 75 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7815 (mm110) REVERT: B 134 ARG cc_start: 0.6514 (mtm-85) cc_final: 0.5669 (pmt170) REVERT: B 138 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8023 (mm-30) REVERT: B 161 SER cc_start: 0.8904 (t) cc_final: 0.8579 (p) REVERT: B 175 GLN cc_start: 0.7679 (mt0) cc_final: 0.7026 (mm110) REVERT: B 180 PHE cc_start: 0.4379 (OUTLIER) cc_final: 0.2021 (p90) REVERT: B 189 SER cc_start: 0.8395 (p) cc_final: 0.8145 (m) REVERT: B 205 ASP cc_start: 0.7025 (p0) cc_final: 0.6720 (p0) REVERT: B 212 ASP cc_start: 0.6693 (t0) cc_final: 0.6417 (t0) REVERT: B 214 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8617 (tpp80) REVERT: B 217 MET cc_start: 0.7777 (ptt) cc_final: 0.7280 (ppp) REVERT: B 220 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: B 239 ASN cc_start: 0.7205 (m-40) cc_final: 0.6831 (t0) REVERT: B 246 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7871 (t0) REVERT: B 254 ASP cc_start: 0.7723 (t0) cc_final: 0.7478 (t0) REVERT: B 298 ASP cc_start: 0.7899 (t70) cc_final: 0.7470 (t70) REVERT: B 303 ASP cc_start: 0.6574 (t0) cc_final: 0.6102 (p0) REVERT: B 339 TRP cc_start: 0.8547 (m100) cc_final: 0.7969 (m-10) REVERT: G 21 MET cc_start: 0.6994 (mtt) cc_final: 0.6542 (tmm) REVERT: G 27 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7495 (mtt90) REVERT: N 105 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6582 (mtm180) outliers start: 27 outliers final: 13 residues processed: 120 average time/residue: 0.4532 time to fit residues: 57.7560 Evaluate side-chains 115 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.178252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131298 restraints weight = 9542.678| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.20 r_work: 0.3649 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8716 Z= 0.123 Angle : 0.511 8.137 11804 Z= 0.265 Chirality : 0.041 0.149 1334 Planarity : 0.003 0.049 1453 Dihedral : 6.095 57.145 1274 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.34 % Allowed : 13.49 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 1024 helix: 2.64 (0.25), residues: 429 sheet: 0.08 (0.33), residues: 234 loop : -0.96 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.008 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8712) covalent geometry : angle 0.51050 / 0.26 (11796) SS BOND : bond 0.00098 / 0.05 ( 4) SS BOND : angle 0.71645 / 0.44 ( 8) hydrogen bonds : bond 0.04330 / 2.87 ( 452) hydrogen bonds : angle 4.32823 / 3.01 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: R 132 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 60 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6456 (mpt) REVERT: A 221 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7555 (mtp) REVERT: A 229 ASP cc_start: 0.8026 (t0) cc_final: 0.7513 (t0) REVERT: A 314 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7212 (pm20) REVERT: A 317 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8023 (ptt-90) REVERT: A 392 GLU cc_start: 0.7980 (tt0) cc_final: 0.7269 (tp30) REVERT: B 46 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.6232 (mtp-110) REVERT: B 68 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.7025 (mmm-85) REVERT: B 134 ARG cc_start: 0.6511 (mtm-85) cc_final: 0.5658 (pmt170) REVERT: B 138 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8001 (mm-30) REVERT: B 161 SER cc_start: 0.8916 (t) cc_final: 0.8634 (p) REVERT: B 175 GLN cc_start: 0.7684 (mt0) cc_final: 0.7028 (mm110) REVERT: B 180 PHE cc_start: 0.4503 (OUTLIER) cc_final: 0.2062 (p90) REVERT: B 189 SER cc_start: 0.8398 (p) cc_final: 0.8149 (m) REVERT: B 205 ASP cc_start: 0.7029 (p0) cc_final: 0.6730 (p0) REVERT: B 214 ARG cc_start: 0.8856 (tpp80) cc_final: 0.8653 (tpp80) REVERT: B 217 MET cc_start: 0.7770 (ptt) cc_final: 0.7347 (ppp) REVERT: B 239 ASN cc_start: 0.7172 (m-40) cc_final: 0.6937 (t0) REVERT: B 246 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7878 (t0) REVERT: B 254 ASP cc_start: 0.7712 (t0) cc_final: 0.6890 (p0) REVERT: B 298 ASP cc_start: 0.7900 (t70) cc_final: 0.7231 (t0) REVERT: B 339 TRP cc_start: 0.8569 (m100) cc_final: 0.7943 (m-10) REVERT: G 21 MET cc_start: 0.6924 (mtt) cc_final: 0.6481 (tmm) REVERT: N 38 ARG cc_start: 0.7595 (ptt180) cc_final: 0.7014 (ptt-90) REVERT: N 105 ARG cc_start: 0.7265 (mtm180) cc_final: 0.6604 (mtm180) outliers start: 30 outliers final: 11 residues processed: 115 average time/residue: 0.4775 time to fit residues: 58.4626 Evaluate side-chains 104 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 185 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.174555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128058 restraints weight = 9751.272| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.20 r_work: 0.3608 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8716 Z= 0.144 Angle : 0.537 8.898 11804 Z= 0.278 Chirality : 0.041 0.153 1334 Planarity : 0.004 0.048 1453 Dihedral : 6.235 56.826 1274 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.68 % Allowed : 14.60 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 1024 helix: 2.67 (0.25), residues: 427 sheet: 0.02 (0.33), residues: 234 loop : -1.03 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.013 0.001 TYR B 59 PHE 0.013 0.001 PHE B 199 TRP 0.011 0.001 TRP R 80 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8712) covalent geometry : angle 0.53711 / 0.28 (11796) SS BOND : bond 0.00117 / 0.06 ( 4) SS BOND : angle 0.81489 / 0.49 ( 8) hydrogen bonds : bond 0.04546 / 3.02 ( 452) hydrogen bonds : angle 4.35840 / 3.03 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: R 132 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7579 (mt-10) REVERT: R 136 THR cc_start: 0.5692 (OUTLIER) cc_final: 0.5350 (p) REVERT: A 34 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6683 (ttpt) REVERT: A 60 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6593 (mpt) REVERT: A 221 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: A 229 ASP cc_start: 0.8030 (t0) cc_final: 0.7509 (t0) REVERT: A 314 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7369 (pm20) REVERT: A 317 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8034 (ptt-90) REVERT: A 392 GLU cc_start: 0.8095 (tt0) cc_final: 0.7402 (tp30) REVERT: B 46 ARG cc_start: 0.6917 (ttm-80) cc_final: 0.6376 (mtp-110) REVERT: B 58 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7988 (mm) REVERT: B 118 ASP cc_start: 0.8165 (p0) cc_final: 0.7944 (p0) REVERT: B 138 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8018 (mm-30) REVERT: B 161 SER cc_start: 0.9052 (t) cc_final: 0.8758 (p) REVERT: B 175 GLN cc_start: 0.7770 (mt0) cc_final: 0.7242 (mp10) REVERT: B 180 PHE cc_start: 0.5089 (OUTLIER) cc_final: 0.2889 (p90) REVERT: B 189 SER cc_start: 0.8474 (p) cc_final: 0.8229 (m) REVERT: B 205 ASP cc_start: 0.7212 (p0) cc_final: 0.6906 (p0) REVERT: B 214 ARG cc_start: 0.8884 (tpp80) cc_final: 0.8603 (tpp80) REVERT: B 217 MET cc_start: 0.7890 (ptt) cc_final: 0.7534 (ppp) REVERT: B 239 ASN cc_start: 0.7358 (m-40) cc_final: 0.7089 (t0) REVERT: B 246 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7906 (t0) REVERT: B 254 ASP cc_start: 0.7826 (t0) cc_final: 0.7088 (p0) REVERT: B 298 ASP cc_start: 0.8087 (t70) cc_final: 0.7522 (t70) REVERT: B 339 TRP cc_start: 0.8656 (m100) cc_final: 0.8074 (m-10) REVERT: G 21 MET cc_start: 0.6952 (mtt) cc_final: 0.6520 (tmm) REVERT: N 38 ARG cc_start: 0.7786 (ptt180) cc_final: 0.7328 (ptt-90) REVERT: N 105 ARG cc_start: 0.7425 (mtm180) cc_final: 0.6706 (mtm180) outliers start: 24 outliers final: 10 residues processed: 112 average time/residue: 0.4830 time to fit residues: 57.6551 Evaluate side-chains 108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.175787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129906 restraints weight = 9595.405| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.14 r_work: 0.3630 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 8716 Z= 0.129 Angle : 0.519 8.413 11804 Z= 0.269 Chirality : 0.041 0.147 1334 Planarity : 0.004 0.050 1453 Dihedral : 6.105 59.606 1274 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.68 % Allowed : 15.05 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.27), residues: 1024 helix: 2.74 (0.25), residues: 428 sheet: 0.03 (0.33), residues: 234 loop : -0.96 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.010 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP R 80 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8712) covalent geometry : angle 0.51847 / 0.27 (11796) SS BOND : bond 0.00102 / 0.05 ( 4) SS BOND : angle 0.66516 / 0.40 ( 8) hydrogen bonds : bond 0.04373 / 2.90 ( 452) hydrogen bonds : angle 4.28179 / 2.98 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: R 136 THR cc_start: 0.5491 (OUTLIER) cc_final: 0.5160 (p) REVERT: A 60 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6327 (mpt) REVERT: A 229 ASP cc_start: 0.7966 (t0) cc_final: 0.7415 (t0) REVERT: A 314 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7350 (pm20) REVERT: A 317 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8011 (ptt-90) REVERT: A 392 GLU cc_start: 0.8000 (tt0) cc_final: 0.7222 (tp30) REVERT: B 46 ARG cc_start: 0.6855 (ttm-80) cc_final: 0.6353 (mtp-110) REVERT: B 58 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7850 (mm) REVERT: B 138 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7967 (mm-30) REVERT: B 161 SER cc_start: 0.9027 (t) cc_final: 0.8733 (p) REVERT: B 175 GLN cc_start: 0.7652 (mt0) cc_final: 0.7144 (mp10) REVERT: B 180 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.2838 (p90) REVERT: B 188 MET cc_start: 0.7274 (mmm) cc_final: 0.6742 (mmm) REVERT: B 189 SER cc_start: 0.8455 (p) cc_final: 0.8177 (m) REVERT: B 205 ASP cc_start: 0.7068 (p0) cc_final: 0.6771 (p0) REVERT: B 214 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8617 (tpp80) REVERT: B 217 MET cc_start: 0.7759 (ptt) cc_final: 0.7406 (ppp) REVERT: B 220 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: B 239 ASN cc_start: 0.7364 (m-40) cc_final: 0.7149 (t0) REVERT: B 246 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7860 (t0) REVERT: B 254 ASP cc_start: 0.7791 (t0) cc_final: 0.6974 (p0) REVERT: B 298 ASP cc_start: 0.7915 (t70) cc_final: 0.7333 (t70) REVERT: B 339 TRP cc_start: 0.8617 (m100) cc_final: 0.7989 (m-10) REVERT: G 21 MET cc_start: 0.6873 (mtt) cc_final: 0.6488 (tmm) REVERT: N 38 ARG cc_start: 0.7570 (ptt180) cc_final: 0.7075 (ptm-80) REVERT: N 105 ARG cc_start: 0.7405 (mtm180) cc_final: 0.6689 (mtm180) outliers start: 24 outliers final: 12 residues processed: 112 average time/residue: 0.4888 time to fit residues: 58.3690 Evaluate side-chains 108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.177496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.131716 restraints weight = 9594.133| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.15 r_work: 0.3654 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 8716 Z= 0.117 Angle : 0.520 8.972 11804 Z= 0.270 Chirality : 0.040 0.147 1334 Planarity : 0.004 0.050 1453 Dihedral : 5.803 55.076 1274 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.90 % Allowed : 16.28 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.27), residues: 1024 helix: 2.82 (0.25), residues: 428 sheet: -0.05 (0.32), residues: 238 loop : -0.90 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.008 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.009 0.001 TRP R 80 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8712) covalent geometry : angle 0.51948 / 0.27 (11796) SS BOND : bond 0.00081 / 0.04 ( 4) SS BOND : angle 0.61008 / 0.37 ( 8) hydrogen bonds : bond 0.04244 / 2.81 ( 452) hydrogen bonds : angle 4.21239 / 2.93 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: R 136 THR cc_start: 0.5442 (OUTLIER) cc_final: 0.5091 (p) REVERT: A 60 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6401 (mpt) REVERT: A 229 ASP cc_start: 0.7880 (t0) cc_final: 0.7340 (t0) REVERT: A 314 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7450 (pm20) REVERT: A 317 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8033 (ptt-90) REVERT: A 392 GLU cc_start: 0.7986 (tt0) cc_final: 0.7207 (tp30) REVERT: B 46 ARG cc_start: 0.6841 (ttm-80) cc_final: 0.6354 (mtp-110) REVERT: B 58 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7830 (mm) REVERT: B 138 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7959 (mm-30) REVERT: B 161 SER cc_start: 0.8968 (t) cc_final: 0.8759 (p) REVERT: B 175 GLN cc_start: 0.7652 (mt0) cc_final: 0.7006 (mm110) REVERT: B 180 PHE cc_start: 0.4813 (OUTLIER) cc_final: 0.2778 (p90) REVERT: B 188 MET cc_start: 0.7290 (mmm) cc_final: 0.6726 (mmm) REVERT: B 189 SER cc_start: 0.8533 (p) cc_final: 0.8162 (m) REVERT: B 205 ASP cc_start: 0.6985 (p0) cc_final: 0.6686 (p0) REVERT: B 214 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8405 (mmt180) REVERT: B 217 MET cc_start: 0.7731 (ptt) cc_final: 0.7375 (ppp) REVERT: B 220 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: B 239 ASN cc_start: 0.7263 (m-40) cc_final: 0.7033 (t0) REVERT: B 246 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7862 (t0) REVERT: B 254 ASP cc_start: 0.7737 (t0) cc_final: 0.6959 (p0) REVERT: B 298 ASP cc_start: 0.7859 (t70) cc_final: 0.7287 (t70) REVERT: B 339 TRP cc_start: 0.8607 (m100) cc_final: 0.7949 (m-10) REVERT: G 21 MET cc_start: 0.6889 (mtt) cc_final: 0.6567 (tmm) REVERT: N 38 ARG cc_start: 0.7722 (ptt180) cc_final: 0.7251 (ptm-80) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 0.5210 time to fit residues: 56.8134 Evaluate side-chains 105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.177747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132115 restraints weight = 9540.928| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.13 r_work: 0.3672 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8716 Z= 0.115 Angle : 0.511 8.636 11804 Z= 0.266 Chirality : 0.040 0.146 1334 Planarity : 0.004 0.051 1453 Dihedral : 5.469 54.221 1274 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.90 % Allowed : 16.16 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.27), residues: 1024 helix: 2.86 (0.25), residues: 428 sheet: -0.04 (0.33), residues: 227 loop : -0.81 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.008 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.009 0.001 TRP R 80 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8712) covalent geometry : angle 0.51112 / 0.27 (11796) SS BOND : bond 0.00073 / 0.04 ( 4) SS BOND : angle 0.56153 / 0.34 ( 8) hydrogen bonds : bond 0.04122 / 2.73 ( 452) hydrogen bonds : angle 4.15624 / 2.89 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 36 SER cc_start: 0.7723 (t) cc_final: 0.7456 (m) REVERT: A 60 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6461 (mpt) REVERT: A 221 MET cc_start: 0.7285 (tpt) cc_final: 0.6183 (tpt) REVERT: A 229 ASP cc_start: 0.7908 (t0) cc_final: 0.7347 (t0) REVERT: A 314 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7498 (pm20) REVERT: A 317 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8019 (ptt-90) REVERT: A 392 GLU cc_start: 0.8019 (tt0) cc_final: 0.7241 (tp30) REVERT: B 46 ARG cc_start: 0.6858 (ttm-80) cc_final: 0.6412 (mtp-110) REVERT: B 58 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7894 (mm) REVERT: B 118 ASP cc_start: 0.8058 (p0) cc_final: 0.7823 (p0) REVERT: B 180 PHE cc_start: 0.4857 (OUTLIER) cc_final: 0.2799 (p90) REVERT: B 188 MET cc_start: 0.7323 (mmm) cc_final: 0.6771 (mmm) REVERT: B 189 SER cc_start: 0.8547 (p) cc_final: 0.8179 (m) REVERT: B 205 ASP cc_start: 0.6943 (p0) cc_final: 0.6646 (p0) REVERT: B 214 ARG cc_start: 0.8901 (tpp80) cc_final: 0.8421 (mmt180) REVERT: B 217 MET cc_start: 0.7754 (ptt) cc_final: 0.7406 (ppp) REVERT: B 239 ASN cc_start: 0.7250 (m-40) cc_final: 0.6952 (t0) REVERT: B 246 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7861 (t0) REVERT: B 254 ASP cc_start: 0.7765 (t0) cc_final: 0.7097 (p0) REVERT: B 298 ASP cc_start: 0.7919 (t70) cc_final: 0.7141 (t0) REVERT: B 339 TRP cc_start: 0.8613 (m100) cc_final: 0.7959 (m-10) REVERT: G 21 MET cc_start: 0.6888 (mtt) cc_final: 0.6618 (tmm) REVERT: N 38 ARG cc_start: 0.7774 (ptt180) cc_final: 0.7302 (ptm-80) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.5571 time to fit residues: 61.8370 Evaluate side-chains 105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 185 ASN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.178750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133582 restraints weight = 9498.994| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.12 r_work: 0.3676 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 8716 Z= 0.107 Angle : 0.499 9.361 11804 Z= 0.259 Chirality : 0.040 0.147 1334 Planarity : 0.004 0.051 1453 Dihedral : 5.267 53.623 1274 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.90 % Allowed : 16.61 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.27), residues: 1024 helix: 3.06 (0.25), residues: 421 sheet: 0.03 (0.33), residues: 227 loop : -0.67 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.007 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP R 123 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 8712) covalent geometry : angle 0.49903 / 0.26 (11796) SS BOND : bond 0.00068 / 0.03 ( 4) SS BOND : angle 0.52589 / 0.32 ( 8) hydrogen bonds : bond 0.03990 / 2.65 ( 452) hydrogen bonds : angle 4.11481 / 2.86 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.04 seconds wall clock time: 39 minutes 57.74 seconds (2397.74 seconds total)