Starting phenix.real_space_refine on Sun Jun 15 12:58:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wkd_32565/06_2025/7wkd_32565.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wkd_32565/06_2025/7wkd_32565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wkd_32565/06_2025/7wkd_32565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wkd_32565/06_2025/7wkd_32565.map" model { file = "/net/cci-nas-00/data/ceres_data/7wkd_32565/06_2025/7wkd_32565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wkd_32565/06_2025/7wkd_32565.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 63 5.16 5 C 5610 2.51 5 N 1504 2.21 5 O 1626 1.98 5 H 8727 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17530 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3794 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5103 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3479 Classifications: {'peptide': 230} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 827 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4279 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.47, per 1000 atoms: 0.54 Number of scatterers: 17530 At special positions: 0 Unit cell: (121.68, 89.44, 123.76, 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) S 63 16.00 O 1626 8.00 N 1504 7.00 C 5610 6.00 H 8727 1.00 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: 4.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.782A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.454A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.584A pdb=" N ASP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.987A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.563A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.731A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 52 Processing helix chain 'R' and resid 58 through 89 removed outlier: 3.580A pdb=" N MET R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 93 through 129 removed outlier: 3.593A pdb=" N SER R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 removed outlier: 3.669A pdb=" N PHE R 135 " --> pdb=" O ILE R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 158 Processing helix chain 'R' and resid 158 through 163 removed outlier: 4.088A pdb=" N PHE R 162 " --> pdb=" O MET R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 187 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 220 Processing helix chain 'R' and resid 263 through 290 Proline residue: R 281 - end of helix removed outlier: 3.672A pdb=" N VAL R 287 " --> pdb=" O ARG R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 320 Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 324 through 335 removed outlier: 3.512A pdb=" N ARG R 328 " --> pdb=" O SER R 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.563A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.236A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.463A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.879A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.007A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 180 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.095A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.932A pdb=" N SER B 250 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.584A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.017A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.017A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.064A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 165 through 166 removed outlier: 3.732A pdb=" N ASP R 165 " --> pdb=" O GLY R 180 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1260 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: 9.42 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8677 1.03 - 1.23: 55 1.23 - 1.42: 3814 1.42 - 1.62: 5072 1.62 - 1.81: 94 Bond restraints: 17712 Sorted by residual: bond pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta sigma weight residual 1.530 1.224 0.306 2.00e-02 2.50e+03 2.33e+02 bond pdb=" N LPD C 3 " pdb=" CA LPD C 3 " ideal model delta sigma weight residual 1.466 1.686 -0.220 1.50e-02 4.44e+03 2.15e+02 bond pdb=" CG PCA C 1 " pdb=" CD PCA C 1 " ideal model delta sigma weight residual 1.517 1.282 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C PCA C 1 " pdb=" N HIS C 2 " ideal model delta sigma weight residual 1.329 1.486 -0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" N LPD C 3 " pdb=" CD LPD C 3 " ideal model delta sigma weight residual 1.473 1.322 0.151 1.40e-02 5.10e+03 1.17e+02 ... (remaining 17707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 31792 2.67 - 5.35: 60 5.35 - 8.02: 4 8.02 - 10.69: 1 10.69 - 13.37: 1 Bond angle restraints: 31858 Sorted by residual: angle pdb=" CA PCA C 1 " pdb=" N PCA C 1 " pdb=" H PCA C 1 " ideal model delta sigma weight residual 114.00 127.37 -13.37 3.00e+00 1.11e-01 1.99e+01 angle pdb=" CB HIS C 2 " pdb=" CG HIS C 2 " pdb=" CD2 HIS C 2 " ideal model delta sigma weight residual 131.20 126.08 5.12 1.30e+00 5.92e-01 1.55e+01 angle pdb=" N PCA C 1 " pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta sigma weight residual 110.50 104.42 6.08 1.70e+00 3.46e-01 1.28e+01 angle pdb=" CA PCA C 1 " pdb=" N PCA C 1 " pdb=" CD PCA C 1 " ideal model delta sigma weight residual 114.17 105.29 8.88 3.00e+00 1.11e-01 8.76e+00 angle pdb=" N LPD C 3 " pdb=" CA LPD C 3 " pdb=" CB LPD C 3 " ideal model delta sigma weight residual 103.00 106.04 -3.04 1.10e+00 8.26e-01 7.62e+00 ... (remaining 31853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.93: 8172 26.93 - 53.86: 145 53.86 - 80.79: 41 80.79 - 107.72: 2 107.72 - 134.65: 1 Dihedral angle restraints: 8361 sinusoidal: 4471 harmonic: 3890 Sorted by residual: dihedral pdb=" N LPD C 3 " pdb=" CA LPD C 3 " pdb=" CB LPD C 3 " pdb=" HB3 LPD C 3 " ideal model delta sinusoidal sigma weight residual 279.27 144.62 134.65 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" N LPD C 3 " pdb=" CA LPD C 3 " pdb=" CB LPD C 3 " pdb=" HB2 LPD C 3 " ideal model delta sinusoidal sigma weight residual 159.47 -93.22 -107.31 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" N PCA C 1 " pdb=" C PCA C 1 " pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta harmonic sigma weight residual 122.80 114.78 8.02 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 8358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 912 0.028 - 0.055: 302 0.055 - 0.083: 87 0.083 - 0.110: 50 0.110 - 0.138: 30 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA HIS C 2 " pdb=" N HIS C 2 " pdb=" C HIS C 2 " pdb=" CB HIS C 2 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 86 " pdb=" N ILE B 86 " pdb=" C ILE B 86 " pdb=" CB ILE B 86 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL E 199 " pdb=" N VAL E 199 " pdb=" C VAL E 199 " pdb=" CB VAL E 199 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1378 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.77e-01 pdb=" N PRO E 74 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.014 5.00e-02 4.00e+02 2.06e-02 6.77e-01 pdb=" N PRO B 241 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 98 " -0.013 5.00e-02 4.00e+02 1.92e-02 5.92e-01 pdb=" N PRO B 99 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.011 5.00e-02 4.00e+02 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1498 2.23 - 2.83: 40190 2.83 - 3.42: 46760 3.42 - 4.01: 64054 4.01 - 4.60: 98630 Nonbonded interactions: 251132 Sorted by model distance: nonbonded pdb=" O THR G 5 " pdb=" H ALA G 9 " model vdw 1.643 2.450 nonbonded pdb=" HE2 HIS B 316 " pdb=" OG1 THR B 334 " model vdw 1.654 2.450 nonbonded pdb="HD22 ASN E 169 " pdb=" OH TYR E 173 " model vdw 1.665 2.450 nonbonded pdb=" H ARG E 86 " pdb=" OD2 ASP E 89 " model vdw 1.669 2.450 nonbonded pdb=" HG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 1.672 2.450 ... (remaining 251127 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: 0.710 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: 0.310 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 43.260 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 : 0.007 0.306 8985 Z= 0.410 Angle : 0.408 8.882 12171 Z= 0.235 Chirality : 0.037 0.138 1381 Planarity : 0.002 0.022 1536 Dihedral : 7.824 81.535 3230 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.31 % Allowed : 2.92 % Favored : 96.77 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1097 helix: 0.04 (0.25), residues: 385 sheet: -1.34 (0.30), residues: 251 loop : -1.95 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.001 0.000 HIS A 329 PHE 0.007 0.001 PHE A 189 TYR 0.004 0.000 TYR E 228 ARG 0.001 0.000 ARG R 57 Details of bonding type rmsd hydrogen bonds : bond 0.13116 ( 443) hydrogen bonds : angle 6.31725 ( 1260) covalent geometry : bond 0.00722 ( 8985) covalent geometry : angle 0.40812 (12171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.7974 (tptt) cc_final: 0.7769 (tptt) REVERT: A 276 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6779 (tm-30) REVERT: B 35 LEU cc_start: 0.6859 (tp) cc_final: 0.6623 (tt) REVERT: B 133 THR cc_start: 0.8063 (p) cc_final: 0.7725 (t) REVERT: B 203 LEU cc_start: 0.7683 (mt) cc_final: 0.7442 (mp) REVERT: B 239 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 244 ASN cc_start: 0.7569 (m-40) cc_final: 0.7338 (m110) REVERT: B 251 ASP cc_start: 0.5791 (p0) cc_final: 0.5280 (p0) REVERT: B 252 ASP cc_start: 0.5060 (t0) cc_final: 0.4729 (t0) REVERT: E 167 HIS cc_start: 0.7542 (t70) cc_final: 0.7303 (t-90) REVERT: E 184 SER cc_start: 0.7816 (p) cc_final: 0.7579 (t) REVERT: G 47 ASP cc_start: 0.7390 (t0) cc_final: 0.7089 (t0) REVERT: R 131 ILE cc_start: 0.7288 (mm) cc_final: 0.7067 (mm) REVERT: R 263 GLN cc_start: 0.5626 (pm20) cc_final: 0.4815 (pm20) REVERT: R 319 ILE cc_start: 0.7599 (tp) cc_final: 0.7217 (pt) outliers start: 3 outliers final: 0 residues processed: 344 average time/residue: 0.5751 time to fit residues: 270.9280 Evaluate side-chains 300 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 245 ASN A 324 HIS B 225 GLN B 273 ASN B 300 ASN R 43 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130590 restraints weight = 36363.281| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.91 r_work: 0.3599 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8985 Z= 0.220 Angle : 0.602 5.803 12171 Z= 0.320 Chirality : 0.041 0.174 1381 Planarity : 0.005 0.036 1536 Dihedral : 4.136 56.855 1227 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.40 % Allowed : 10.43 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1097 helix: 1.19 (0.26), residues: 378 sheet: -1.17 (0.30), residues: 258 loop : -1.01 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 248 HIS 0.010 0.002 HIS A 324 PHE 0.021 0.002 PHE B 240 TYR 0.019 0.002 TYR A 306 ARG 0.008 0.001 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 443) hydrogen bonds : angle 5.07691 ( 1260) covalent geometry : bond 0.00482 ( 8985) covalent geometry : angle 0.60213 (12171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8148 (ttpt) REVERT: B 53 ARG cc_start: 0.8223 (mmt180) cc_final: 0.8001 (mmp80) REVERT: B 62 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8062 (mtmm) REVERT: B 123 ASP cc_start: 0.7683 (t0) cc_final: 0.7153 (t0) REVERT: B 129 TYR cc_start: 0.8236 (m-80) cc_final: 0.7142 (m-80) REVERT: B 194 SER cc_start: 0.7989 (p) cc_final: 0.7772 (t) REVERT: B 195 LEU cc_start: 0.7672 (mt) cc_final: 0.7404 (mt) REVERT: B 203 LEU cc_start: 0.8244 (mt) cc_final: 0.8038 (mp) REVERT: B 219 ARG cc_start: 0.7496 (mtt180) cc_final: 0.7291 (mtt180) REVERT: B 224 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7256 (mtp-110) REVERT: B 244 ASN cc_start: 0.8074 (m-40) cc_final: 0.7814 (m110) REVERT: B 345 ASN cc_start: 0.6966 (t0) cc_final: 0.6760 (t0) REVERT: E 167 HIS cc_start: 0.8132 (t70) cc_final: 0.7677 (t-90) REVERT: E 220 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7242 (mm-30) REVERT: G 47 ASP cc_start: 0.7902 (t0) cc_final: 0.7593 (t0) REVERT: R 113 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.7430 (t) REVERT: R 298 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7321 (mm-30) REVERT: R 312 ASN cc_start: 0.8157 (t0) cc_final: 0.7912 (t0) REVERT: R 319 ILE cc_start: 0.7721 (tp) cc_final: 0.7464 (pt) outliers start: 23 outliers final: 17 residues processed: 329 average time/residue: 0.5547 time to fit residues: 245.9954 Evaluate side-chains 310 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 359 ASN B 130 ASN B 225 GLN E 194 ASN R 82 ASN R 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120560 restraints weight = 37036.756| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.88 r_work: 0.3523 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8985 Z= 0.223 Angle : 0.539 5.499 12171 Z= 0.289 Chirality : 0.040 0.216 1381 Planarity : 0.004 0.044 1536 Dihedral : 4.248 59.792 1227 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.23 % Allowed : 13.14 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1097 helix: 1.55 (0.27), residues: 380 sheet: -1.12 (0.29), residues: 267 loop : -0.89 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.014 0.002 HIS A 324 PHE 0.017 0.002 PHE B 240 TYR 0.015 0.002 TYR E 190 ARG 0.007 0.001 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 443) hydrogen bonds : angle 5.03396 ( 1260) covalent geometry : bond 0.00487 ( 8985) covalent geometry : angle 0.53894 (12171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7346 (mtm110) REVERT: A 32 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7407 (mtm-85) REVERT: A 241 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8119 (ttpt) REVERT: A 276 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 311 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6322 (tp30) REVERT: B 53 ARG cc_start: 0.8262 (mmt180) cc_final: 0.8021 (mmp80) REVERT: B 123 ASP cc_start: 0.7715 (t0) cc_final: 0.7197 (t0) REVERT: B 178 THR cc_start: 0.8132 (m) cc_final: 0.7892 (p) REVERT: B 194 SER cc_start: 0.8023 (p) cc_final: 0.7819 (p) REVERT: B 219 ARG cc_start: 0.7534 (mtt180) cc_final: 0.7329 (mtt180) REVERT: B 235 ASN cc_start: 0.7654 (m-40) cc_final: 0.7391 (m-40) REVERT: B 239 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 244 ASN cc_start: 0.8101 (m-40) cc_final: 0.7862 (m-40) REVERT: B 251 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: B 321 SER cc_start: 0.7899 (t) cc_final: 0.7532 (p) REVERT: B 322 CYS cc_start: 0.7804 (p) cc_final: 0.7491 (p) REVERT: B 345 ASN cc_start: 0.7238 (t0) cc_final: 0.7034 (t0) REVERT: E 66 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8202 (mtm110) REVERT: E 167 HIS cc_start: 0.8231 (t70) cc_final: 0.7933 (t70) REVERT: E 220 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7378 (mm-30) REVERT: R 267 MET cc_start: 0.7769 (tpp) cc_final: 0.7527 (tpp) REVERT: R 298 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7304 (mm-30) REVERT: R 312 ASN cc_start: 0.8271 (t0) cc_final: 0.7980 (t0) outliers start: 31 outliers final: 21 residues processed: 318 average time/residue: 0.5391 time to fit residues: 229.1234 Evaluate side-chains 313 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 238 ASN A 324 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115554 restraints weight = 36956.207| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.84 r_work: 0.3460 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8985 Z= 0.341 Angle : 0.604 5.930 12171 Z= 0.329 Chirality : 0.043 0.248 1381 Planarity : 0.005 0.056 1536 Dihedral : 4.710 58.923 1227 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.13 % Allowed : 17.52 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1097 helix: 1.21 (0.26), residues: 380 sheet: -1.01 (0.29), residues: 267 loop : -0.91 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP R 160 HIS 0.009 0.002 HIS E 232 PHE 0.026 0.002 PHE B 240 TYR 0.021 0.002 TYR E 190 ARG 0.004 0.001 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 443) hydrogen bonds : angle 5.25056 ( 1260) covalent geometry : bond 0.00740 ( 8985) covalent geometry : angle 0.60384 (12171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 313 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7404 (mtm110) REVERT: A 233 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 241 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8147 (ttpt) REVERT: A 276 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 348 ASP cc_start: 0.7909 (t70) cc_final: 0.7469 (t0) REVERT: B 53 ARG cc_start: 0.8375 (mmt180) cc_final: 0.8108 (mmp80) REVERT: B 102 SER cc_start: 0.8136 (t) cc_final: 0.7651 (p) REVERT: B 123 ASP cc_start: 0.7813 (t0) cc_final: 0.7283 (t0) REVERT: B 129 TYR cc_start: 0.8483 (m-80) cc_final: 0.7875 (m-80) REVERT: B 135 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 160 ASN cc_start: 0.7952 (t0) cc_final: 0.7654 (t0) REVERT: B 175 ASP cc_start: 0.7750 (t0) cc_final: 0.7386 (t0) REVERT: B 178 THR cc_start: 0.8170 (m) cc_final: 0.7954 (p) REVERT: B 205 VAL cc_start: 0.8540 (p) cc_final: 0.8339 (m) REVERT: B 235 ASN cc_start: 0.7727 (m-40) cc_final: 0.7453 (m110) REVERT: B 244 ASN cc_start: 0.8126 (m-40) cc_final: 0.7874 (m-40) REVERT: B 251 ASP cc_start: 0.8233 (m-30) cc_final: 0.8021 (m-30) REVERT: B 321 SER cc_start: 0.7981 (t) cc_final: 0.7632 (p) REVERT: B 336 SER cc_start: 0.8205 (t) cc_final: 0.7807 (m) REVERT: E 10 LEU cc_start: 0.8609 (tt) cc_final: 0.8387 (tt) REVERT: E 56 THR cc_start: 0.8436 (p) cc_final: 0.8187 (p) REVERT: E 220 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7461 (mm-30) REVERT: R 52 ARG cc_start: 0.7730 (mpt180) cc_final: 0.7510 (mpt180) REVERT: R 298 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7277 (mm-30) REVERT: R 312 ASN cc_start: 0.8169 (t0) cc_final: 0.7885 (t0) outliers start: 30 outliers final: 23 residues processed: 323 average time/residue: 0.5163 time to fit residues: 221.1591 Evaluate side-chains 320 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 295 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115580 restraints weight = 37083.944| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.88 r_work: 0.3458 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8985 Z= 0.229 Angle : 0.537 5.028 12171 Z= 0.288 Chirality : 0.041 0.227 1381 Planarity : 0.004 0.042 1536 Dihedral : 4.597 57.994 1227 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.23 % Allowed : 18.46 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1097 helix: 1.37 (0.27), residues: 379 sheet: -0.84 (0.30), residues: 258 loop : -0.73 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 104 HIS 0.006 0.002 HIS E 232 PHE 0.019 0.002 PHE B 240 TYR 0.014 0.002 TYR E 190 ARG 0.005 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 443) hydrogen bonds : angle 5.06011 ( 1260) covalent geometry : bond 0.00501 ( 8985) covalent geometry : angle 0.53706 (12171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 302 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7872 (mttm) REVERT: A 29 VAL cc_start: 0.8441 (t) cc_final: 0.8183 (p) REVERT: A 31 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7359 (mtm110) REVERT: A 233 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 241 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8102 (ttpt) REVERT: A 276 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 342 ILE cc_start: 0.8186 (mm) cc_final: 0.7975 (mt) REVERT: B 53 ARG cc_start: 0.8391 (mmt180) cc_final: 0.8151 (mmp80) REVERT: B 102 SER cc_start: 0.8178 (t) cc_final: 0.7715 (p) REVERT: B 123 ASP cc_start: 0.7845 (t0) cc_final: 0.7317 (t0) REVERT: B 129 TYR cc_start: 0.8413 (m-80) cc_final: 0.7793 (m-80) REVERT: B 135 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 175 ASP cc_start: 0.7773 (t0) cc_final: 0.7445 (t0) REVERT: B 244 ASN cc_start: 0.8068 (m-40) cc_final: 0.7815 (m110) REVERT: B 246 PHE cc_start: 0.8173 (p90) cc_final: 0.7961 (p90) REVERT: B 321 SER cc_start: 0.7910 (t) cc_final: 0.7579 (p) REVERT: B 336 SER cc_start: 0.8105 (t) cc_final: 0.7730 (m) REVERT: E 10 LEU cc_start: 0.8622 (tt) cc_final: 0.8418 (tt) REVERT: E 86 ARG cc_start: 0.8132 (ptp-170) cc_final: 0.7849 (mtm-85) REVERT: E 220 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7459 (mm-30) REVERT: R 265 THR cc_start: 0.8084 (t) cc_final: 0.7863 (m) REVERT: R 298 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7295 (mm-30) REVERT: R 327 PHE cc_start: 0.8072 (t80) cc_final: 0.7766 (t80) outliers start: 31 outliers final: 25 residues processed: 311 average time/residue: 0.5245 time to fit residues: 216.6628 Evaluate side-chains 324 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 322 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 246 ASN A 329 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118024 restraints weight = 36882.227| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.83 r_work: 0.3472 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8985 Z= 0.161 Angle : 0.510 5.509 12171 Z= 0.270 Chirality : 0.039 0.208 1381 Planarity : 0.004 0.036 1536 Dihedral : 4.471 58.158 1227 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.23 % Allowed : 19.92 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1097 helix: 1.62 (0.26), residues: 380 sheet: -0.83 (0.30), residues: 258 loop : -0.61 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS C 2 PHE 0.013 0.001 PHE B 240 TYR 0.013 0.002 TYR B 64 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 443) hydrogen bonds : angle 4.88797 ( 1260) covalent geometry : bond 0.00354 ( 8985) covalent geometry : angle 0.50996 (12171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7843 (mttm) REVERT: A 29 VAL cc_start: 0.8425 (t) cc_final: 0.8152 (p) REVERT: A 31 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7309 (mtm110) REVERT: A 33 THR cc_start: 0.8556 (t) cc_final: 0.8263 (p) REVERT: A 185 PHE cc_start: 0.7693 (t80) cc_final: 0.7293 (t80) REVERT: A 226 ASP cc_start: 0.7848 (t0) cc_final: 0.7510 (t70) REVERT: A 233 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7385 (mp) REVERT: A 276 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 298 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7405 (t0) REVERT: A 342 ILE cc_start: 0.8185 (mm) cc_final: 0.7943 (mt) REVERT: B 49 GLN cc_start: 0.7162 (tm-30) cc_final: 0.6929 (tm-30) REVERT: B 53 ARG cc_start: 0.8382 (mmt180) cc_final: 0.8165 (mmp80) REVERT: B 102 SER cc_start: 0.8178 (t) cc_final: 0.7706 (p) REVERT: B 123 ASP cc_start: 0.7820 (t0) cc_final: 0.7278 (t0) REVERT: B 129 TYR cc_start: 0.8385 (m-80) cc_final: 0.7676 (m-80) REVERT: B 135 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7957 (mp0) REVERT: B 139 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7401 (mtp-110) REVERT: B 244 ASN cc_start: 0.8064 (m-40) cc_final: 0.7806 (m-40) REVERT: B 321 SER cc_start: 0.7846 (t) cc_final: 0.7572 (p) REVERT: E 10 LEU cc_start: 0.8619 (tt) cc_final: 0.8414 (tt) REVERT: E 56 THR cc_start: 0.8431 (p) cc_final: 0.8206 (p) REVERT: E 86 ARG cc_start: 0.8096 (ptp-170) cc_final: 0.7850 (mtm-85) REVERT: E 220 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7465 (mm-30) REVERT: R 265 THR cc_start: 0.8046 (t) cc_final: 0.7833 (m) REVERT: R 298 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7199 (mm-30) REVERT: R 322 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7915 (mp) REVERT: R 323 MET cc_start: 0.7792 (mmm) cc_final: 0.7565 (mmm) REVERT: R 327 PHE cc_start: 0.8047 (t80) cc_final: 0.7750 (t80) outliers start: 31 outliers final: 20 residues processed: 315 average time/residue: 0.5798 time to fit residues: 248.7402 Evaluate side-chains 320 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 246 ASN A 329 HIS B 80 GLN R 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120433 restraints weight = 36925.742| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.85 r_work: 0.3475 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8985 Z= 0.147 Angle : 0.498 5.237 12171 Z= 0.265 Chirality : 0.039 0.202 1381 Planarity : 0.004 0.040 1536 Dihedral : 4.392 57.969 1227 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.13 % Allowed : 19.19 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1097 helix: 1.79 (0.27), residues: 380 sheet: -0.87 (0.29), residues: 260 loop : -0.51 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.004 0.001 HIS C 2 PHE 0.015 0.001 PHE B 246 TYR 0.025 0.001 TYR B 64 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 443) hydrogen bonds : angle 4.81163 ( 1260) covalent geometry : bond 0.00323 ( 8985) covalent geometry : angle 0.49845 (12171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7826 (mttm) REVERT: A 29 VAL cc_start: 0.8428 (t) cc_final: 0.8170 (p) REVERT: A 31 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7293 (mtm110) REVERT: A 185 PHE cc_start: 0.7707 (t80) cc_final: 0.7307 (t80) REVERT: A 226 ASP cc_start: 0.7913 (t0) cc_final: 0.7712 (t70) REVERT: A 233 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7362 (mp) REVERT: A 276 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 298 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7394 (t0) REVERT: A 342 ILE cc_start: 0.8210 (mm) cc_final: 0.7972 (mt) REVERT: B 22 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 49 GLN cc_start: 0.7126 (tm-30) cc_final: 0.6895 (tm-30) REVERT: B 53 ARG cc_start: 0.8373 (mmt180) cc_final: 0.8168 (mmp80) REVERT: B 102 SER cc_start: 0.8185 (t) cc_final: 0.7727 (p) REVERT: B 123 ASP cc_start: 0.7822 (t0) cc_final: 0.7233 (t0) REVERT: B 129 TYR cc_start: 0.8388 (m-80) cc_final: 0.7664 (m-80) REVERT: B 135 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 244 ASN cc_start: 0.8047 (m-40) cc_final: 0.7784 (m-40) REVERT: B 321 SER cc_start: 0.7911 (t) cc_final: 0.7593 (p) REVERT: E 10 LEU cc_start: 0.8626 (tt) cc_final: 0.8416 (tt) REVERT: E 86 ARG cc_start: 0.8084 (ptp-170) cc_final: 0.7832 (mtm-85) REVERT: E 220 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7414 (mm-30) REVERT: R 265 THR cc_start: 0.8056 (t) cc_final: 0.7854 (m) REVERT: R 298 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7219 (mm-30) REVERT: R 322 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7839 (mp) REVERT: R 327 PHE cc_start: 0.8065 (t80) cc_final: 0.7777 (t80) outliers start: 30 outliers final: 24 residues processed: 309 average time/residue: 0.5227 time to fit residues: 213.4327 Evaluate side-chains 328 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 106 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN A 329 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN R 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116478 restraints weight = 36887.442| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.84 r_work: 0.3451 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8985 Z= 0.264 Angle : 0.554 5.399 12171 Z= 0.299 Chirality : 0.041 0.226 1381 Planarity : 0.004 0.042 1536 Dihedral : 4.607 58.213 1227 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.34 % Allowed : 19.40 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1097 helix: 1.50 (0.26), residues: 387 sheet: -0.79 (0.30), residues: 258 loop : -0.55 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 46 HIS 0.005 0.001 HIS C 2 PHE 0.019 0.002 PHE B 240 TYR 0.026 0.002 TYR B 64 ARG 0.008 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 443) hydrogen bonds : angle 4.97256 ( 1260) covalent geometry : bond 0.00576 ( 8985) covalent geometry : angle 0.55351 (12171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 303 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8402 (t) cc_final: 0.8125 (p) REVERT: A 31 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7323 (mtm110) REVERT: A 33 THR cc_start: 0.8530 (t) cc_final: 0.8193 (p) REVERT: A 185 PHE cc_start: 0.7697 (t80) cc_final: 0.7268 (t80) REVERT: A 226 ASP cc_start: 0.7950 (t0) cc_final: 0.7718 (t0) REVERT: A 233 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7352 (mp) REVERT: A 276 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 342 ILE cc_start: 0.8183 (mm) cc_final: 0.7947 (mt) REVERT: B 49 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6937 (tm-30) REVERT: B 53 ARG cc_start: 0.8399 (mmt180) cc_final: 0.8173 (mmp80) REVERT: B 102 SER cc_start: 0.8218 (t) cc_final: 0.7753 (p) REVERT: B 123 ASP cc_start: 0.7825 (t0) cc_final: 0.7227 (t0) REVERT: B 129 TYR cc_start: 0.8491 (m-80) cc_final: 0.7745 (m-80) REVERT: B 135 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 244 ASN cc_start: 0.8073 (m-40) cc_final: 0.7812 (m-40) REVERT: B 321 SER cc_start: 0.7945 (t) cc_final: 0.7615 (p) REVERT: E 10 LEU cc_start: 0.8630 (tt) cc_final: 0.8423 (tt) REVERT: E 86 ARG cc_start: 0.8101 (ptp-170) cc_final: 0.7845 (mtm-85) REVERT: E 220 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7459 (mm-30) REVERT: R 187 TYR cc_start: 0.7183 (m-80) cc_final: 0.6852 (m-80) REVERT: R 298 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7261 (mm-30) REVERT: R 312 ASN cc_start: 0.8069 (t0) cc_final: 0.7831 (t0) REVERT: R 322 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7881 (mp) REVERT: R 327 PHE cc_start: 0.8073 (t80) cc_final: 0.7781 (t80) outliers start: 32 outliers final: 27 residues processed: 313 average time/residue: 0.5269 time to fit residues: 218.0501 Evaluate side-chains 329 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 322 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 246 ASN A 329 HIS ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116892 restraints weight = 36921.094| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.87 r_work: 0.3474 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8985 Z= 0.146 Angle : 0.521 4.950 12171 Z= 0.277 Chirality : 0.040 0.226 1381 Planarity : 0.004 0.039 1536 Dihedral : 4.499 58.183 1227 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.02 % Allowed : 20.33 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1097 helix: 1.66 (0.26), residues: 387 sheet: -0.77 (0.30), residues: 261 loop : -0.45 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 344 HIS 0.004 0.001 HIS C 2 PHE 0.012 0.001 PHE B 240 TYR 0.025 0.002 TYR B 64 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 443) hydrogen bonds : angle 4.88580 ( 1260) covalent geometry : bond 0.00322 ( 8985) covalent geometry : angle 0.52072 (12171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8389 (t) cc_final: 0.8109 (p) REVERT: A 31 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7297 (mtm110) REVERT: A 33 THR cc_start: 0.8563 (t) cc_final: 0.8208 (p) REVERT: A 185 PHE cc_start: 0.7537 (t80) cc_final: 0.7157 (t80) REVERT: A 197 HIS cc_start: 0.7683 (m170) cc_final: 0.7419 (m-70) REVERT: A 226 ASP cc_start: 0.7936 (t0) cc_final: 0.7730 (t0) REVERT: A 233 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7335 (mp) REVERT: A 248 TRP cc_start: 0.8587 (m100) cc_final: 0.8324 (m100) REVERT: A 276 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 298 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7428 (t70) REVERT: A 342 ILE cc_start: 0.8160 (mm) cc_final: 0.7931 (mt) REVERT: B 49 GLN cc_start: 0.7128 (tm-30) cc_final: 0.6900 (tm-30) REVERT: B 53 ARG cc_start: 0.8390 (mmt180) cc_final: 0.8181 (mmp80) REVERT: B 102 SER cc_start: 0.8206 (t) cc_final: 0.7743 (p) REVERT: B 123 ASP cc_start: 0.7755 (t0) cc_final: 0.7163 (t0) REVERT: B 129 TYR cc_start: 0.8414 (m-80) cc_final: 0.7736 (m-80) REVERT: B 139 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7396 (mtp-110) REVERT: B 244 ASN cc_start: 0.8069 (m-40) cc_final: 0.7806 (m-40) REVERT: B 321 SER cc_start: 0.7989 (t) cc_final: 0.7649 (p) REVERT: E 86 ARG cc_start: 0.8084 (ptp-170) cc_final: 0.7847 (mtm-85) REVERT: E 220 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7477 (mm-30) REVERT: R 187 TYR cc_start: 0.7165 (m-80) cc_final: 0.6796 (m-80) REVERT: R 298 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7247 (mm-30) REVERT: R 322 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7853 (mp) REVERT: R 327 PHE cc_start: 0.8074 (t80) cc_final: 0.7785 (t80) outliers start: 29 outliers final: 25 residues processed: 304 average time/residue: 0.5454 time to fit residues: 218.6133 Evaluate side-chains 324 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 329 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117463 restraints weight = 36747.774| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.85 r_work: 0.3462 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8985 Z= 0.201 Angle : 0.538 5.347 12171 Z= 0.287 Chirality : 0.041 0.214 1381 Planarity : 0.004 0.038 1536 Dihedral : 4.580 58.271 1227 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.13 % Allowed : 20.65 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1097 helix: 1.64 (0.26), residues: 386 sheet: -0.75 (0.30), residues: 260 loop : -0.40 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 46 HIS 0.005 0.001 HIS A 329 PHE 0.015 0.002 PHE B 240 TYR 0.022 0.002 TYR B 64 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 443) hydrogen bonds : angle 4.92298 ( 1260) covalent geometry : bond 0.00442 ( 8985) covalent geometry : angle 0.53751 (12171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8368 (t) cc_final: 0.8082 (p) REVERT: A 33 THR cc_start: 0.8557 (t) cc_final: 0.8201 (p) REVERT: A 185 PHE cc_start: 0.7537 (t80) cc_final: 0.7173 (t80) REVERT: A 197 HIS cc_start: 0.7679 (m170) cc_final: 0.7427 (m-70) REVERT: A 233 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 276 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 342 ILE cc_start: 0.8174 (mm) cc_final: 0.7959 (mt) REVERT: B 47 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.7089 (mtp-110) REVERT: B 49 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 53 ARG cc_start: 0.8396 (mmt180) cc_final: 0.8170 (mmp80) REVERT: B 102 SER cc_start: 0.8192 (t) cc_final: 0.7763 (p) REVERT: B 123 ASP cc_start: 0.7750 (t0) cc_final: 0.7172 (t0) REVERT: B 129 TYR cc_start: 0.8477 (m-80) cc_final: 0.7819 (m-80) REVERT: B 139 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7389 (mtp-110) REVERT: B 244 ASN cc_start: 0.8067 (m-40) cc_final: 0.7799 (m-40) REVERT: B 321 SER cc_start: 0.8008 (t) cc_final: 0.7652 (p) REVERT: E 86 ARG cc_start: 0.8089 (ptp-170) cc_final: 0.7871 (mtm-85) REVERT: E 220 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7463 (mm-30) REVERT: R 187 TYR cc_start: 0.7184 (m-80) cc_final: 0.6788 (m-80) REVERT: R 298 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7255 (mm-30) REVERT: R 322 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7865 (mp) REVERT: R 327 PHE cc_start: 0.8063 (t80) cc_final: 0.7781 (t80) outliers start: 30 outliers final: 25 residues processed: 302 average time/residue: 0.5574 time to fit residues: 224.7163 Evaluate side-chains 316 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 329 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119900 restraints weight = 36846.846| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.89 r_work: 0.3467 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8985 Z= 0.165 Angle : 0.528 6.065 12171 Z= 0.280 Chirality : 0.040 0.206 1381 Planarity : 0.004 0.041 1536 Dihedral : 4.508 57.725 1227 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.82 % Allowed : 20.86 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1097 helix: 1.74 (0.26), residues: 385 sheet: -0.71 (0.30), residues: 260 loop : -0.33 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 302 HIS 0.005 0.001 HIS A 329 PHE 0.013 0.001 PHE B 240 TYR 0.018 0.002 TYR B 64 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 443) hydrogen bonds : angle 4.85042 ( 1260) covalent geometry : bond 0.00364 ( 8985) covalent geometry : angle 0.52830 (12171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11991.20 seconds wall clock time: 208 minutes 57.67 seconds (12537.67 seconds total)