Starting phenix.real_space_refine on Wed Sep 17 12:13:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xoi_38530/09_2025/8xoi_38530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xoi_38530/09_2025/8xoi_38530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xoi_38530/09_2025/8xoi_38530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xoi_38530/09_2025/8xoi_38530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xoi_38530/09_2025/8xoi_38530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xoi_38530/09_2025/8xoi_38530.map" } resolution = 3.2 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= 0.008 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5566 2.51 5 N 1522 2.21 5 O 1609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8753 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1866 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2554 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1735 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 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: "R" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2162 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain breaks: 3 Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 8753 At special positions: 0 Unit cell: (113.526, 121.023, 109.242, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1609 8.00 N 1522 7.00 C 5566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 414.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 39.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.603A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.746A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.540A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.529A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 53 through 87 removed outlier: 4.612A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix removed outlier: 3.518A pdb=" N PHE R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 91 Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.549A pdb=" N LEU R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 removed outlier: 4.308A pdb=" N TYR R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 161 Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 247 Processing helix chain 'R' and resid 254 through 285 Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.902A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 329 through 342 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.418A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.852A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.576A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.927A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.238A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.910A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.384A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.792A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.545A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.545A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.470A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.174A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1293 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: 1.45 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 1616 1.45 - 1.57: 4875 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8930 Sorted by residual: bond pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 1.522 1.552 -0.030 1.39e-02 5.18e+03 4.77e+00 bond pdb=" C ASN R 77 " pdb=" O ASN R 77 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.16e-02 7.43e+03 4.14e+00 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.25e-02 6.40e+03 3.68e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 11615 1.21 - 2.41: 393 2.41 - 3.62: 65 3.62 - 4.82: 17 4.82 - 6.03: 2 Bond angle restraints: 12092 Sorted by residual: angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" CB MET E 192 " ideal model delta sigma weight residual 114.17 109.27 4.90 1.14e+00 7.69e-01 1.85e+01 angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 108.76 102.73 6.03 1.69e+00 3.50e-01 1.27e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.65 117.90 4.75 1.60e+00 3.91e-01 8.80e+00 angle pdb=" CA ASN R 77 " pdb=" C ASN R 77 " pdb=" O ASN R 77 " ideal model delta sigma weight residual 120.70 117.77 2.93 1.03e+00 9.43e-01 8.09e+00 angle pdb=" N ILE A 235 " pdb=" CA ILE A 235 " pdb=" C ILE A 235 " ideal model delta sigma weight residual 112.98 109.45 3.53 1.25e+00 6.40e-01 7.99e+00 ... (remaining 12087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4680 17.51 - 35.01: 481 35.01 - 52.52: 111 52.52 - 70.03: 19 70.03 - 87.54: 7 Dihedral angle restraints: 5298 sinusoidal: 2063 harmonic: 3235 Sorted by residual: dihedral pdb=" CA PHE R 326 " pdb=" C PHE R 326 " pdb=" N LEU R 327 " pdb=" CA LEU R 327 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 378 " pdb=" CB ASP A 378 " pdb=" CG ASP A 378 " pdb=" OD1 ASP A 378 " ideal model delta sinusoidal sigma weight residual -30.00 -89.81 59.81 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 943 0.033 - 0.067: 304 0.067 - 0.100: 75 0.100 - 0.133: 50 0.133 - 0.166: 5 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA TYR A 391 " pdb=" N TYR A 391 " pdb=" C TYR A 391 " pdb=" CB TYR A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1374 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 321 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 236 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C PRO B 236 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO B 236 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 237 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 233 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C CYS B 233 " -0.029 2.00e-02 2.50e+03 pdb=" O CYS B 233 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE B 234 " 0.010 2.00e-02 2.50e+03 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1062 2.75 - 3.29: 8908 3.29 - 3.82: 14943 3.82 - 4.36: 17970 4.36 - 4.90: 31189 Nonbonded interactions: 74072 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU A 21 " pdb=" OG SER E 52 " model vdw 2.226 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.271 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.309 3.040 ... (remaining 74067 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.003 0.034 8930 Z= 0.153 Angle : 0.539 6.030 12092 Z= 0.315 Chirality : 0.040 0.166 1377 Planarity : 0.004 0.053 1534 Dihedral : 15.215 87.536 3202 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.32 % Allowed : 13.19 % Favored : 86.50 % 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 aren not related in a simple way. whole: 0.82 (0.26), residues: 1091 helix: 2.06 (0.25), residues: 417 sheet: -0.54 (0.31), residues: 262 loop : -0.20 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 42 TYR 0.011 0.001 TYR E 103 PHE 0.014 0.001 PHE R 326 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8930) covalent geometry : angle 0.53928 (12092) hydrogen bonds : bond 0.15374 ( 454) hydrogen bonds : angle 6.60765 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.7991 (ttp) cc_final: 0.7719 (tmm) REVERT: B 212 ASP cc_start: 0.7801 (t70) cc_final: 0.7342 (t70) REVERT: B 217 MET cc_start: 0.7918 (ppp) cc_final: 0.7660 (ppp) REVERT: B 337 LYS cc_start: 0.9066 (mttm) cc_final: 0.8782 (mttm) REVERT: G 20 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7363 (ptmt) REVERT: R 64 LEU cc_start: 0.7654 (tp) cc_final: 0.7434 (mt) REVERT: R 314 PHE cc_start: 0.7976 (m-80) cc_final: 0.7551 (m-80) outliers start: 3 outliers final: 3 residues processed: 162 average time/residue: 0.1156 time to fit residues: 24.7384 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 99 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 227 GLN B 259 GLN R 200 HIS R 282 HIS R 341 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.162073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112960 restraints weight = 10727.616| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.28 r_work: 0.3018 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8930 Z= 0.147 Angle : 0.551 8.064 12092 Z= 0.295 Chirality : 0.042 0.146 1377 Planarity : 0.004 0.039 1534 Dihedral : 5.049 59.443 1213 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.53 % Allowed : 13.40 % Favored : 84.07 % 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 aren not related in a simple way. whole: 0.99 (0.25), residues: 1091 helix: 2.26 (0.25), residues: 409 sheet: -0.41 (0.31), residues: 257 loop : -0.15 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 42 TYR 0.009 0.001 TYR E 190 PHE 0.016 0.002 PHE R 326 TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS R 200 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8930) covalent geometry : angle 0.55065 (12092) hydrogen bonds : bond 0.04274 ( 454) hydrogen bonds : angle 4.97109 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7871 (mtp-110) REVERT: A 209 GLU cc_start: 0.8167 (tt0) cc_final: 0.7743 (mt-10) REVERT: A 386 MET cc_start: 0.8353 (ttp) cc_final: 0.8094 (tmm) REVERT: B 3 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.4011 (pt0) REVERT: B 212 ASP cc_start: 0.7957 (t70) cc_final: 0.7653 (t70) REVERT: E 160 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6212 (mtp85) REVERT: G 48 ASP cc_start: 0.8378 (t0) cc_final: 0.8169 (t0) outliers start: 24 outliers final: 12 residues processed: 183 average time/residue: 0.1023 time to fit residues: 25.0550 Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 44 GLN E 179 GLN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 HIS ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.161436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110834 restraints weight = 10617.157| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.18 r_work: 0.3063 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8930 Z= 0.188 Angle : 0.552 7.538 12092 Z= 0.294 Chirality : 0.043 0.239 1377 Planarity : 0.004 0.030 1534 Dihedral : 5.095 59.425 1211 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.53 % Allowed : 15.51 % Favored : 81.96 % 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 aren not related in a simple way. whole: 0.83 (0.25), residues: 1091 helix: 2.08 (0.25), residues: 413 sheet: -0.36 (0.31), residues: 257 loop : -0.30 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.012 0.002 TYR R 156 PHE 0.019 0.002 PHE R 326 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8930) covalent geometry : angle 0.55152 (12092) hydrogen bonds : bond 0.04172 ( 454) hydrogen bonds : angle 4.77072 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8104 (tt0) cc_final: 0.7748 (mt-10) REVERT: A 265 ARG cc_start: 0.7592 (ptm160) cc_final: 0.7277 (ptm-80) REVERT: A 386 MET cc_start: 0.8311 (ttp) cc_final: 0.8085 (tmm) REVERT: B 212 ASP cc_start: 0.8014 (t70) cc_final: 0.7743 (t70) REVERT: E 59 TYR cc_start: 0.8250 (m-80) cc_final: 0.7880 (m-80) REVERT: E 67 ARG cc_start: 0.6783 (ttp80) cc_final: 0.6544 (mtp85) REVERT: E 160 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6339 (mtp85) REVERT: G 48 ASP cc_start: 0.8456 (t0) cc_final: 0.8210 (t0) REVERT: R 54 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6557 (mp10) REVERT: R 77 ASN cc_start: 0.8428 (m110) cc_final: 0.7992 (m110) REVERT: R 183 MET cc_start: 0.7089 (ttt) cc_final: 0.6359 (tpp) outliers start: 24 outliers final: 18 residues processed: 162 average time/residue: 0.1002 time to fit residues: 21.8316 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 54 GLN Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 220 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 80 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.165751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126935 restraints weight = 10507.401| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.23 r_work: 0.3016 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8930 Z= 0.103 Angle : 0.482 5.553 12092 Z= 0.257 Chirality : 0.040 0.138 1377 Planarity : 0.003 0.031 1534 Dihedral : 4.813 59.665 1211 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.85 % Allowed : 14.77 % Favored : 82.38 % 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 aren not related in a simple way. whole: 1.07 (0.25), residues: 1091 helix: 2.46 (0.25), residues: 407 sheet: -0.32 (0.31), residues: 252 loop : -0.29 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.008 0.001 TYR E 190 PHE 0.015 0.001 PHE R 269 TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8930) covalent geometry : angle 0.48151 (12092) hydrogen bonds : bond 0.03541 ( 454) hydrogen bonds : angle 4.43518 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7912 (tt0) cc_final: 0.7563 (mt-10) REVERT: A 213 GLN cc_start: 0.8120 (tt0) cc_final: 0.7691 (tt0) REVERT: A 230 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6349 (tm-30) REVERT: A 293 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7333 (mmtt) REVERT: A 386 MET cc_start: 0.8107 (ttp) cc_final: 0.7837 (tmm) REVERT: B 212 ASP cc_start: 0.7768 (t70) cc_final: 0.7510 (t70) REVERT: B 217 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7568 (ppp) REVERT: E 59 TYR cc_start: 0.8157 (m-80) cc_final: 0.7780 (m-80) REVERT: E 160 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6244 (mtp85) REVERT: R 54 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: R 77 ASN cc_start: 0.8266 (m110) cc_final: 0.7861 (m-40) REVERT: R 183 MET cc_start: 0.6924 (ttt) cc_final: 0.6128 (tpp) outliers start: 27 outliers final: 12 residues processed: 173 average time/residue: 0.1004 time to fit residues: 23.6663 Evaluate side-chains 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 54 GLN Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN R 245 HIS R 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111696 restraints weight = 10798.591| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.18 r_work: 0.2999 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8930 Z= 0.225 Angle : 0.572 7.228 12092 Z= 0.304 Chirality : 0.043 0.154 1377 Planarity : 0.004 0.032 1534 Dihedral : 5.061 59.548 1211 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.27 % Allowed : 15.51 % Favored : 81.22 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1091 helix: 2.13 (0.25), residues: 413 sheet: -0.41 (0.31), residues: 256 loop : -0.37 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 67 TYR 0.016 0.002 TYR R 156 PHE 0.024 0.002 PHE R 326 TRP 0.012 0.002 TRP A 234 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 8930) covalent geometry : angle 0.57152 (12092) hydrogen bonds : bond 0.04068 ( 454) hydrogen bonds : angle 4.60598 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: A 293 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7613 (mmtt) REVERT: A 386 MET cc_start: 0.8309 (ttp) cc_final: 0.8075 (tmm) REVERT: B 217 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7800 (ppp) REVERT: E 59 TYR cc_start: 0.8258 (m-80) cc_final: 0.7913 (m-80) REVERT: E 160 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6324 (mtp85) REVERT: R 64 LEU cc_start: 0.8051 (tt) cc_final: 0.7757 (mt) REVERT: R 77 ASN cc_start: 0.8460 (m-40) cc_final: 0.7822 (m110) REVERT: R 183 MET cc_start: 0.7017 (ttt) cc_final: 0.6242 (tpp) REVERT: R 283 LEU cc_start: 0.7913 (mt) cc_final: 0.7706 (mt) outliers start: 31 outliers final: 24 residues processed: 167 average time/residue: 0.1028 time to fit residues: 23.3105 Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120799 restraints weight = 10420.290| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.02 r_work: 0.3049 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8930 Z= 0.160 Angle : 0.523 6.930 12092 Z= 0.277 Chirality : 0.041 0.146 1377 Planarity : 0.004 0.033 1534 Dihedral : 4.804 59.666 1211 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.27 % Allowed : 16.24 % Favored : 80.49 % 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 aren not related in a simple way. whole: 0.85 (0.25), residues: 1091 helix: 2.21 (0.25), residues: 413 sheet: -0.34 (0.31), residues: 249 loop : -0.45 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.011 0.001 TYR E 190 PHE 0.017 0.002 PHE R 326 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8930) covalent geometry : angle 0.52264 (12092) hydrogen bonds : bond 0.03762 ( 454) hydrogen bonds : angle 4.48129 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8046 (tt0) cc_final: 0.7528 (mt-10) REVERT: A 213 GLN cc_start: 0.8235 (tt0) cc_final: 0.7811 (tt0) REVERT: A 230 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: A 293 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7522 (mmtt) REVERT: A 386 MET cc_start: 0.8285 (ttp) cc_final: 0.7985 (tmm) REVERT: B 217 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7674 (ppp) REVERT: E 59 TYR cc_start: 0.8257 (m-80) cc_final: 0.7859 (m-80) REVERT: E 180 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7538 (mtt90) REVERT: R 64 LEU cc_start: 0.8070 (tt) cc_final: 0.7720 (mt) REVERT: R 77 ASN cc_start: 0.8454 (m-40) cc_final: 0.8033 (m-40) REVERT: R 183 MET cc_start: 0.6817 (ttt) cc_final: 0.5994 (tpp) REVERT: R 315 SER cc_start: 0.8827 (m) cc_final: 0.8479 (p) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.1032 time to fit residues: 23.0309 Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 260 MET Chi-restraints excluded: chain R residue 265 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131717 restraints weight = 10354.441| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.04 r_work: 0.2968 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8930 Z= 0.151 Angle : 0.522 6.884 12092 Z= 0.277 Chirality : 0.041 0.142 1377 Planarity : 0.003 0.035 1534 Dihedral : 4.656 59.982 1210 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.48 % Allowed : 16.56 % Favored : 79.96 % 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 aren not related in a simple way. whole: 0.88 (0.25), residues: 1091 helix: 2.24 (0.25), residues: 413 sheet: -0.32 (0.31), residues: 249 loop : -0.46 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.011 0.001 TYR E 103 PHE 0.016 0.002 PHE R 314 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS R 282 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8930) covalent geometry : angle 0.52159 (12092) hydrogen bonds : bond 0.03691 ( 454) hydrogen bonds : angle 4.42102 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7918 (tt0) cc_final: 0.7469 (mt-10) REVERT: A 230 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: A 293 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7577 (mmtt) REVERT: A 386 MET cc_start: 0.8184 (ttp) cc_final: 0.7894 (tmm) REVERT: B 217 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7732 (ppp) REVERT: E 59 TYR cc_start: 0.8198 (m-80) cc_final: 0.7809 (m-80) REVERT: E 67 ARG cc_start: 0.6527 (ttp-170) cc_final: 0.6174 (ttp-170) REVERT: E 160 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6166 (mtp85) REVERT: E 180 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7608 (mtt90) REVERT: R 183 MET cc_start: 0.6812 (ttt) cc_final: 0.5998 (tpp) REVERT: R 315 SER cc_start: 0.8810 (m) cc_final: 0.8544 (p) outliers start: 33 outliers final: 25 residues processed: 170 average time/residue: 0.1032 time to fit residues: 23.6838 Evaluate side-chains 176 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 260 MET Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.164242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117201 restraints weight = 10425.345| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.16 r_work: 0.3100 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8930 Z= 0.114 Angle : 0.482 6.682 12092 Z= 0.258 Chirality : 0.040 0.138 1377 Planarity : 0.003 0.037 1534 Dihedral : 4.468 59.975 1210 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.95 % Allowed : 17.30 % Favored : 79.75 % 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 aren not related in a simple way. whole: 0.98 (0.25), residues: 1091 helix: 2.31 (0.25), residues: 413 sheet: -0.24 (0.31), residues: 253 loop : -0.40 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.009 0.001 TYR E 103 PHE 0.012 0.001 PHE A 212 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8930) covalent geometry : angle 0.48220 (12092) hydrogen bonds : bond 0.03506 ( 454) hydrogen bonds : angle 4.29276 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7942 (tt0) cc_final: 0.7476 (mt-10) REVERT: A 213 GLN cc_start: 0.8203 (tt0) cc_final: 0.7995 (tt0) REVERT: A 230 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6361 (tm-30) REVERT: A 293 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7444 (mmtt) REVERT: A 386 MET cc_start: 0.8241 (ttp) cc_final: 0.7979 (tmm) REVERT: B 195 ASP cc_start: 0.7640 (p0) cc_final: 0.7333 (p0) REVERT: B 217 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7702 (ppp) REVERT: E 59 TYR cc_start: 0.8263 (m-80) cc_final: 0.7896 (m-80) REVERT: E 67 ARG cc_start: 0.6385 (ttp-170) cc_final: 0.6031 (ttp-170) REVERT: E 160 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6071 (mtp85) REVERT: E 180 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7634 (mtt90) REVERT: R 70 PHE cc_start: 0.7146 (t80) cc_final: 0.6787 (t80) REVERT: R 77 ASN cc_start: 0.8225 (m-40) cc_final: 0.7958 (m-40) REVERT: R 183 MET cc_start: 0.6824 (ttt) cc_final: 0.5988 (tpp) outliers start: 28 outliers final: 20 residues processed: 171 average time/residue: 0.0982 time to fit residues: 22.6240 Evaluate side-chains 169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 260 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN E 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.164527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125441 restraints weight = 10725.558| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.79 r_work: 0.3021 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8930 Z= 0.107 Angle : 0.484 9.319 12092 Z= 0.256 Chirality : 0.040 0.135 1377 Planarity : 0.003 0.038 1534 Dihedral : 4.358 59.749 1210 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.85 % Allowed : 17.72 % Favored : 79.43 % 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 aren not related in a simple way. whole: 1.06 (0.25), residues: 1091 helix: 2.38 (0.25), residues: 412 sheet: -0.14 (0.31), residues: 253 loop : -0.38 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.009 0.001 TYR E 190 PHE 0.013 0.001 PHE R 70 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8930) covalent geometry : angle 0.48361 (12092) hydrogen bonds : bond 0.03408 ( 454) hydrogen bonds : angle 4.19869 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7724 (tt0) cc_final: 0.7435 (mt-10) REVERT: A 213 GLN cc_start: 0.8129 (tt0) cc_final: 0.7747 (tt0) REVERT: A 230 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: A 293 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7587 (mmtt) REVERT: B 195 ASP cc_start: 0.7622 (p0) cc_final: 0.7337 (p0) REVERT: B 198 LEU cc_start: 0.8865 (mt) cc_final: 0.8631 (mt) REVERT: B 217 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7782 (ppp) REVERT: B 266 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6849 (t-170) REVERT: E 59 TYR cc_start: 0.8139 (m-80) cc_final: 0.7808 (m-80) REVERT: E 67 ARG cc_start: 0.6478 (ttp-170) cc_final: 0.6084 (ttp-170) REVERT: R 70 PHE cc_start: 0.7212 (t80) cc_final: 0.6900 (t80) REVERT: R 77 ASN cc_start: 0.8270 (m-40) cc_final: 0.7146 (m110) REVERT: R 183 MET cc_start: 0.6891 (ttt) cc_final: 0.6128 (tpp) outliers start: 27 outliers final: 21 residues processed: 178 average time/residue: 0.1000 time to fit residues: 24.1013 Evaluate side-chains 174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 260 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124600 restraints weight = 10690.122| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.76 r_work: 0.3036 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8930 Z= 0.118 Angle : 0.489 7.744 12092 Z= 0.259 Chirality : 0.040 0.137 1377 Planarity : 0.003 0.039 1534 Dihedral : 4.386 59.967 1210 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.53 % Allowed : 18.25 % Favored : 79.22 % 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 aren not related in a simple way. whole: 1.08 (0.25), residues: 1091 helix: 2.36 (0.25), residues: 413 sheet: -0.09 (0.31), residues: 253 loop : -0.36 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.010 0.001 TYR E 190 PHE 0.012 0.001 PHE A 212 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8930) covalent geometry : angle 0.48912 (12092) hydrogen bonds : bond 0.03447 ( 454) hydrogen bonds : angle 4.20220 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7688 (tt0) cc_final: 0.7434 (mt-10) REVERT: A 213 GLN cc_start: 0.8147 (tt0) cc_final: 0.7938 (tt0) REVERT: A 230 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: A 293 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7603 (mmtt) REVERT: B 195 ASP cc_start: 0.7640 (p0) cc_final: 0.7370 (p0) REVERT: B 217 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7786 (ppp) REVERT: B 266 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6857 (t-170) REVERT: E 59 TYR cc_start: 0.8135 (m-80) cc_final: 0.7810 (m-80) REVERT: E 67 ARG cc_start: 0.6466 (ttp-170) cc_final: 0.6217 (ttp-170) REVERT: R 70 PHE cc_start: 0.7229 (t80) cc_final: 0.7017 (t80) REVERT: R 77 ASN cc_start: 0.8338 (m-40) cc_final: 0.7225 (m110) REVERT: R 183 MET cc_start: 0.6873 (ttt) cc_final: 0.6115 (tpp) outliers start: 24 outliers final: 19 residues processed: 169 average time/residue: 0.0991 time to fit residues: 22.5848 Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 260 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125512 restraints weight = 10652.726| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.76 r_work: 0.3041 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8930 Z= 0.105 Angle : 0.476 8.361 12092 Z= 0.252 Chirality : 0.040 0.135 1377 Planarity : 0.003 0.041 1534 Dihedral : 4.275 59.666 1210 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.43 % Allowed : 18.14 % Favored : 79.43 % 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 aren not related in a simple way. whole: 1.18 (0.25), residues: 1091 helix: 2.45 (0.25), residues: 412 sheet: -0.03 (0.31), residues: 258 loop : -0.32 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 87 TYR 0.008 0.001 TYR A 339 PHE 0.012 0.001 PHE R 70 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8930) covalent geometry : angle 0.47649 (12092) hydrogen bonds : bond 0.03327 ( 454) hydrogen bonds : angle 4.13234 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.56 seconds wall clock time: 46 minutes 10.79 seconds (2770.79 seconds total)