Starting phenix.real_space_refine on Wed Aug 5 09:23:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24qh_69759/08_2026/24qh_69759.cif Found real_map, /net/cci-nas-00/data/ceres_data/24qh_69759/08_2026/24qh_69759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24qh_69759/08_2026/24qh_69759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24qh_69759/08_2026/24qh_69759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24qh_69759/08_2026/24qh_69759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24qh_69759/08_2026/24qh_69759.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5699 2.51 5 N 1535 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8931 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1716 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2435 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 13, 'TRANS': 293} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 8931 At special positions: 0 Unit cell: (92.65, 121.55, 131.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1638 8.00 N 1535 7.00 C 5699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 457.5 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 36.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.561A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.412A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.582A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.559A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.510A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.640A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.512A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'A' and resid 35 through 67 Processing helix chain 'A' and resid 73 through 90 removed outlier: 4.017A pdb=" N LEU A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 109 through 142 removed outlier: 3.646A pdb=" N THR A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.790A pdb=" N ALA A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.630A pdb=" N CYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 244 removed outlier: 3.591A pdb=" N THR A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.817A pdb=" N LEU A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 293 removed outlier: 3.585A pdb=" N ILE A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 311 through 323 removed outlier: 4.051A pdb=" N ALA A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Proline residue: A 318 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.817A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.632A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.613A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.103A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.769A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.672A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.822A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.664A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.897A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.369A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.567A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.529A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.042A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 177 through 183 removed outlier: 4.110A pdb=" N ARG A 178 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 195 " --> pdb=" O ARG A 178 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2874 1.34 - 1.46: 1701 1.46 - 1.58: 4456 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9115 Sorted by residual: bond pdb=" N GLU A 204 " pdb=" CA GLU A 204 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.19e-02 7.06e+03 2.29e+00 bond pdb=" CG LEU A 49 " pdb=" CD2 LEU A 49 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.56e+00 bond pdb=" C GLY A 203 " pdb=" N GLU A 204 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.27e-02 6.20e+03 1.25e+00 bond pdb=" CB VAL G 16 " pdb=" CG1 VAL G 16 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" CA ALA C 203 " pdb=" C ALA C 203 " ideal model delta sigma weight residual 1.523 1.509 0.014 1.41e-02 5.03e+03 9.83e-01 ... (remaining 9110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 12241 2.42 - 4.85: 106 4.85 - 7.27: 9 7.27 - 9.70: 3 9.70 - 12.12: 1 Bond angle restraints: 12360 Sorted by residual: angle pdb=" C VAL A 141 " pdb=" N HIS A 142 " pdb=" CA HIS A 142 " ideal model delta sigma weight residual 123.00 117.06 5.94 1.38e+00 5.25e-01 1.85e+01 angle pdb=" CA LEU A 49 " pdb=" CB LEU A 49 " pdb=" CG LEU A 49 " ideal model delta sigma weight residual 116.30 128.42 -12.12 3.50e+00 8.16e-02 1.20e+01 angle pdb=" N PRO A 26 " pdb=" CA PRO A 26 " pdb=" C PRO A 26 " ideal model delta sigma weight residual 112.47 118.50 -6.03 2.06e+00 2.36e-01 8.57e+00 angle pdb=" C ALA S 221 " pdb=" N GLU S 222 " pdb=" CA GLU S 222 " ideal model delta sigma weight residual 123.91 128.63 -4.72 1.66e+00 3.63e-01 8.07e+00 angle pdb=" N GLU A 102 " pdb=" CA GLU A 102 " pdb=" C GLU A 102 " ideal model delta sigma weight residual 113.38 110.30 3.08 1.17e+00 7.31e-01 6.94e+00 ... (remaining 12355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 4881 15.98 - 31.96: 421 31.96 - 47.94: 78 47.94 - 63.92: 21 63.92 - 79.90: 8 Dihedral angle restraints: 5409 sinusoidal: 2086 harmonic: 3323 Sorted by residual: dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA HIS A 142 " pdb=" C HIS A 142 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " ideal model delta harmonic sigma weight residual 180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1011 0.040 - 0.081: 305 0.081 - 0.121: 93 0.121 - 0.161: 14 0.161 - 0.202: 2 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CB ILE A 201 " pdb=" CA ILE A 201 " pdb=" CG1 ILE A 201 " pdb=" CG2 ILE A 201 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA PRO A 26 " pdb=" N PRO A 26 " pdb=" C PRO A 26 " pdb=" CB PRO A 26 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA GLU S 222 " pdb=" N GLU S 222 " pdb=" C GLU S 222 " pdb=" CB GLU S 222 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1422 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 207 " -0.012 2.00e-02 2.50e+03 1.21e-02 3.65e+00 pdb=" CG TRP A 207 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 207 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 207 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 207 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 207 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 207 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 207 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 207 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 207 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO S 148 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 107 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 108 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.022 5.00e-02 4.00e+02 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 80 2.62 - 3.19: 7545 3.19 - 3.76: 13099 3.76 - 4.33: 18379 4.33 - 4.90: 31983 Nonbonded interactions: 71086 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.048 3.040 nonbonded pdb=" CG2 VAL A 31 " pdb=" CD1 LEU A 184 " model vdw 2.051 3.880 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.089 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.242 3.040 nonbonded pdb=" ND1 HIS A 112 " pdb=" O CYS A 174 " model vdw 2.251 3.120 ... (remaining 71081 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: 6.020 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9118 Z= 0.153 Angle : 0.604 12.122 12366 Z= 0.327 Chirality : 0.043 0.202 1425 Planarity : 0.004 0.046 1558 Dihedral : 13.115 79.896 3252 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.21 % Allowed : 0.62 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1131 helix: 2.02 (0.27), residues: 383 sheet: 0.70 (0.32), residues: 281 loop : -1.20 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.008 0.001 TYR C 296 PHE 0.012 0.001 PHE A 27 TRP 0.033 0.002 TRP A 207 HIS 0.008 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9115) covalent geometry : angle 0.60359 / 0.33 (12360) SS BOND : bond 0.00519 / 0.24 ( 3) SS BOND : angle 0.81799 / 0.45 ( 6) hydrogen bonds : bond 0.17003 / 11.46 ( 433) hydrogen bonds : angle 6.12895 / 4.38 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.334 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 20 LYS cc_start: 0.8351 (mttp) cc_final: 0.8136 (mttp) outliers start: 2 outliers final: 3 residues processed: 143 average time/residue: 0.6945 time to fit residues: 104.5589 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain A residue 204 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN S 179 GLN S 186 GLN A 80 ASN ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.071889 restraints weight = 17465.922| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.94 r_work: 0.2834 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9118 Z= 0.161 Angle : 0.606 8.693 12366 Z= 0.316 Chirality : 0.044 0.218 1425 Planarity : 0.004 0.035 1558 Dihedral : 6.029 122.945 1249 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.07 % Allowed : 9.41 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1131 helix: 2.28 (0.27), residues: 380 sheet: 0.58 (0.31), residues: 298 loop : -1.14 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.010 0.001 TYR S 190 PHE 0.013 0.001 PHE A 27 TRP 0.022 0.002 TRP A 104 HIS 0.018 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9115) covalent geometry : angle 0.60566 / 0.32 (12360) SS BOND : bond 0.00750 / 0.37 ( 3) SS BOND : angle 1.16642 / 0.63 ( 6) hydrogen bonds : bond 0.04922 / 3.29 ( 433) hydrogen bonds : angle 4.49025 / 3.23 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.333 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8578 (ttpp) REVERT: B 217 MET cc_start: 0.8709 (ptt) cc_final: 0.8357 (ptt) REVERT: G 14 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8948 (mtmm) REVERT: A 116 TYR cc_start: 0.8456 (t80) cc_final: 0.8202 (t80) REVERT: A 190 GLU cc_start: 0.7970 (tp30) cc_final: 0.7747 (tp30) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 0.7136 time to fit residues: 96.2053 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 204 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 ASN A 112 HIS A 142 HIS ** A 290 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.107586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.071244 restraints weight = 17452.016| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.96 r_work: 0.2842 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9118 Z= 0.151 Angle : 0.585 10.675 12366 Z= 0.305 Chirality : 0.044 0.241 1425 Planarity : 0.004 0.036 1558 Dihedral : 4.764 58.734 1246 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.69 % Allowed : 11.48 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1131 helix: 2.37 (0.27), residues: 381 sheet: 0.60 (0.31), residues: 296 loop : -1.22 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 218 TYR 0.010 0.001 TYR S 190 PHE 0.012 0.001 PHE A 27 TRP 0.018 0.002 TRP A 104 HIS 0.017 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9115) covalent geometry : angle 0.58422 / 0.30 (12360) SS BOND : bond 0.00697 / 0.35 ( 3) SS BOND : angle 1.15351 / 0.60 ( 6) hydrogen bonds : bond 0.04529 / 3.02 ( 433) hydrogen bonds : angle 4.26974 / 3.07 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.370 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: B 15 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8562 (ttpp) REVERT: B 217 MET cc_start: 0.8622 (ptt) cc_final: 0.8266 (ptt) REVERT: G 14 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8958 (mtmm) REVERT: A 116 TYR cc_start: 0.8448 (t80) cc_final: 0.8228 (t80) REVERT: A 176 PHE cc_start: 0.8196 (m-10) cc_final: 0.7969 (m-80) REVERT: A 190 GLU cc_start: 0.7958 (tp30) cc_final: 0.7714 (tp30) REVERT: A 207 TRP cc_start: 0.7616 (t60) cc_final: 0.7380 (t60) outliers start: 26 outliers final: 11 residues processed: 132 average time/residue: 0.6153 time to fit residues: 85.8224 Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain A residue 139 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 ASN A 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071299 restraints weight = 17761.273| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.98 r_work: 0.2838 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9118 Z= 0.139 Angle : 0.574 9.351 12366 Z= 0.298 Chirality : 0.043 0.239 1425 Planarity : 0.004 0.037 1558 Dihedral : 4.545 59.426 1243 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.28 % Allowed : 13.24 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1131 helix: 2.48 (0.27), residues: 380 sheet: 0.61 (0.31), residues: 294 loop : -1.20 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 218 TYR 0.010 0.001 TYR S 190 PHE 0.010 0.001 PHE C 189 TRP 0.024 0.001 TRP A 104 HIS 0.017 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9115) covalent geometry : angle 0.57413 / 0.30 (12360) SS BOND : bond 0.00642 / 0.32 ( 3) SS BOND : angle 1.06586 / 0.56 ( 6) hydrogen bonds : bond 0.04243 / 2.84 ( 433) hydrogen bonds : angle 4.12148 / 2.96 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.379 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 32 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7916 (mtm-85) REVERT: B 15 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8666 (ttpp) REVERT: B 215 GLU cc_start: 0.8823 (mp0) cc_final: 0.8382 (mp0) REVERT: B 217 MET cc_start: 0.8797 (ptt) cc_final: 0.8525 (ptt) REVERT: G 14 LYS cc_start: 0.9253 (mtpt) cc_final: 0.8996 (mtmm) REVERT: A 116 TYR cc_start: 0.8531 (t80) cc_final: 0.8317 (t80) REVERT: A 176 PHE cc_start: 0.8185 (m-10) cc_final: 0.7919 (m-10) REVERT: A 190 GLU cc_start: 0.7929 (tp30) cc_final: 0.7719 (tp30) REVERT: A 207 TRP cc_start: 0.7695 (t60) cc_final: 0.7075 (t60) outliers start: 22 outliers final: 12 residues processed: 121 average time/residue: 0.7274 time to fit residues: 92.4734 Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 139 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS G 24 ASN A 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.071785 restraints weight = 17464.830| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.96 r_work: 0.2844 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9118 Z= 0.125 Angle : 0.555 9.710 12366 Z= 0.289 Chirality : 0.043 0.232 1425 Planarity : 0.004 0.047 1558 Dihedral : 4.459 59.996 1243 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.69 % Allowed : 13.03 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1131 helix: 2.55 (0.27), residues: 380 sheet: 0.57 (0.30), residues: 300 loop : -1.12 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 218 TYR 0.010 0.001 TYR S 190 PHE 0.010 0.001 PHE C 189 TRP 0.020 0.001 TRP A 104 HIS 0.017 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9115) covalent geometry : angle 0.55422 / 0.29 (12360) SS BOND : bond 0.00592 / 0.30 ( 3) SS BOND : angle 1.03894 / 0.53 ( 6) hydrogen bonds : bond 0.03976 / 2.66 ( 433) hydrogen bonds : angle 4.00545 / 2.87 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.241 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 32 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7924 (mtm-85) REVERT: B 15 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8689 (ttpp) REVERT: B 172 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8660 (tp30) REVERT: B 215 GLU cc_start: 0.8802 (mp0) cc_final: 0.8289 (mp0) REVERT: G 14 LYS cc_start: 0.9253 (mtpt) cc_final: 0.9017 (mtmm) REVERT: A 176 PHE cc_start: 0.8152 (m-10) cc_final: 0.7877 (m-10) REVERT: A 207 TRP cc_start: 0.7731 (t60) cc_final: 0.7159 (t60) outliers start: 26 outliers final: 11 residues processed: 131 average time/residue: 0.5815 time to fit residues: 80.3528 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 201 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072322 restraints weight = 17555.096| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.95 r_work: 0.2859 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9118 Z= 0.122 Angle : 0.575 12.168 12366 Z= 0.293 Chirality : 0.042 0.231 1425 Planarity : 0.004 0.052 1558 Dihedral : 4.421 59.693 1243 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.59 % Allowed : 14.17 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1131 helix: 2.60 (0.27), residues: 380 sheet: 0.61 (0.30), residues: 299 loop : -1.09 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 218 TYR 0.010 0.001 TYR S 190 PHE 0.011 0.001 PHE A 27 TRP 0.016 0.001 TRP A 104 HIS 0.013 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9115) covalent geometry : angle 0.57500 / 0.29 (12360) SS BOND : bond 0.00570 / 0.29 ( 3) SS BOND : angle 1.02793 / 0.53 ( 6) hydrogen bonds : bond 0.03864 / 2.59 ( 433) hydrogen bonds : angle 3.97923 / 2.85 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.290 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 32 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7883 (mtm-85) REVERT: B 15 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (ttpp) REVERT: B 172 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8574 (tp30) REVERT: G 14 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8995 (mtmm) REVERT: A 27 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: A 176 PHE cc_start: 0.8129 (m-80) cc_final: 0.7834 (m-10) REVERT: A 207 TRP cc_start: 0.7717 (t60) cc_final: 0.7197 (t60) REVERT: A 323 MET cc_start: 0.3514 (OUTLIER) cc_final: 0.2686 (tpt) outliers start: 25 outliers final: 14 residues processed: 128 average time/residue: 0.6243 time to fit residues: 84.2932 Evaluate side-chains 130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 186 GLN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071881 restraints weight = 17517.151| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.94 r_work: 0.2844 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9118 Z= 0.137 Angle : 0.593 12.522 12366 Z= 0.304 Chirality : 0.043 0.235 1425 Planarity : 0.004 0.056 1558 Dihedral : 4.447 59.479 1243 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.48 % Allowed : 15.10 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1131 helix: 2.62 (0.27), residues: 380 sheet: 0.57 (0.30), residues: 300 loop : -1.13 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 218 TYR 0.010 0.001 TYR S 190 PHE 0.012 0.001 PHE A 27 TRP 0.015 0.001 TRP A 104 HIS 0.012 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9115) covalent geometry : angle 0.59310 / 0.30 (12360) SS BOND : bond 0.00614 / 0.31 ( 3) SS BOND : angle 1.09835 / 0.55 ( 6) hydrogen bonds : bond 0.03946 / 2.63 ( 433) hydrogen bonds : angle 3.97180 / 2.84 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.231 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 32 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7866 (mtm-85) REVERT: B 15 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8647 (ttpp) REVERT: B 172 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8574 (tp30) REVERT: G 14 LYS cc_start: 0.9241 (mtpt) cc_final: 0.9004 (mtmm) REVERT: A 27 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: A 176 PHE cc_start: 0.8139 (m-80) cc_final: 0.7868 (m-10) REVERT: A 182 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 207 TRP cc_start: 0.7727 (t60) cc_final: 0.7218 (t60) REVERT: A 323 MET cc_start: 0.3425 (OUTLIER) cc_final: 0.2539 (tpt) outliers start: 24 outliers final: 15 residues processed: 125 average time/residue: 0.6666 time to fit residues: 87.8487 Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS B 259 GLN S 186 GLN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071685 restraints weight = 17651.225| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.94 r_work: 0.2829 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9118 Z= 0.162 Angle : 0.621 11.837 12366 Z= 0.316 Chirality : 0.044 0.239 1425 Planarity : 0.004 0.052 1558 Dihedral : 4.557 59.277 1243 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.00 % Allowed : 14.79 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1131 helix: 2.61 (0.27), residues: 381 sheet: 0.56 (0.30), residues: 299 loop : -1.17 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 218 TYR 0.010 0.001 TYR C 296 PHE 0.014 0.001 PHE A 27 TRP 0.015 0.001 TRP A 104 HIS 0.007 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 9115) covalent geometry : angle 0.62063 / 0.32 (12360) SS BOND : bond 0.00678 / 0.34 ( 3) SS BOND : angle 1.24172 / 0.62 ( 6) hydrogen bonds : bond 0.04226 / 2.80 ( 433) hydrogen bonds : angle 4.03455 / 2.89 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.289 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: B 15 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8621 (ttpp) REVERT: G 14 LYS cc_start: 0.9237 (mtpt) cc_final: 0.9000 (mtmm) REVERT: A 27 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: A 176 PHE cc_start: 0.8184 (m-80) cc_final: 0.7902 (m-10) REVERT: A 207 TRP cc_start: 0.7734 (t60) cc_final: 0.7223 (t60) REVERT: A 323 MET cc_start: 0.3359 (OUTLIER) cc_final: 0.2458 (tpt) outliers start: 29 outliers final: 17 residues processed: 127 average time/residue: 0.6536 time to fit residues: 87.5314 Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 99 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS B 259 GLN S 186 GLN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.108118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072059 restraints weight = 17475.880| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.95 r_work: 0.2844 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9118 Z= 0.143 Angle : 0.617 13.572 12366 Z= 0.315 Chirality : 0.043 0.238 1425 Planarity : 0.004 0.061 1558 Dihedral : 4.525 58.973 1243 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.48 % Allowed : 15.51 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1131 helix: 2.63 (0.27), residues: 381 sheet: 0.58 (0.30), residues: 298 loop : -1.16 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 218 TYR 0.010 0.001 TYR C 296 PHE 0.013 0.001 PHE A 27 TRP 0.013 0.001 TRP A 104 HIS 0.009 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9115) covalent geometry : angle 0.61623 / 0.31 (12360) SS BOND : bond 0.00632 / 0.32 ( 3) SS BOND : angle 1.15333 / 0.57 ( 6) hydrogen bonds : bond 0.04030 / 2.68 ( 433) hydrogen bonds : angle 4.00320 / 2.87 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.332 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: B 15 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8636 (ttpp) REVERT: G 14 LYS cc_start: 0.9234 (mtpt) cc_final: 0.9025 (mtmm) REVERT: A 27 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: A 37 LEU cc_start: 0.7853 (mm) cc_final: 0.7426 (tt) REVERT: A 176 PHE cc_start: 0.8133 (m-80) cc_final: 0.7880 (m-10) REVERT: A 207 TRP cc_start: 0.7715 (t60) cc_final: 0.7209 (t60) REVERT: A 323 MET cc_start: 0.3390 (OUTLIER) cc_final: 0.2471 (tpt) outliers start: 24 outliers final: 17 residues processed: 130 average time/residue: 0.7159 time to fit residues: 98.0411 Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 HIS S 186 GLN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071934 restraints weight = 17607.106| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.95 r_work: 0.2845 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9118 Z= 0.147 Angle : 0.630 13.273 12366 Z= 0.319 Chirality : 0.043 0.240 1425 Planarity : 0.004 0.064 1558 Dihedral : 4.537 58.491 1243 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.07 % Allowed : 15.72 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1131 helix: 2.63 (0.27), residues: 381 sheet: 0.58 (0.30), residues: 303 loop : -1.14 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 218 TYR 0.011 0.001 TYR C 296 PHE 0.013 0.001 PHE A 27 TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9115) covalent geometry : angle 0.63009 / 0.32 (12360) SS BOND : bond 0.00646 / 0.33 ( 3) SS BOND : angle 1.18049 / 0.58 ( 6) hydrogen bonds : bond 0.04051 / 2.68 ( 433) hydrogen bonds : angle 4.01662 / 2.88 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.366 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 32 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: B 15 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8638 (ttpp) REVERT: B 172 GLU cc_start: 0.8870 (pt0) cc_final: 0.8584 (tp30) REVERT: A 27 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: A 37 LEU cc_start: 0.7809 (mm) cc_final: 0.7370 (tt) REVERT: A 104 TRP cc_start: 0.7574 (t-100) cc_final: 0.7363 (t-100) REVERT: A 176 PHE cc_start: 0.8116 (m-80) cc_final: 0.7902 (m-10) REVERT: A 207 TRP cc_start: 0.7745 (t60) cc_final: 0.7249 (t60) REVERT: A 323 MET cc_start: 0.3415 (OUTLIER) cc_final: 0.2636 (tpt) outliers start: 20 outliers final: 17 residues processed: 126 average time/residue: 0.7184 time to fit residues: 95.4311 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.6980 chunk 56 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 0.0770 chunk 77 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 294 ASN S 186 GLN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.109525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073811 restraints weight = 17286.350| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.96 r_work: 0.2899 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9118 Z= 0.105 Angle : 0.583 13.264 12366 Z= 0.298 Chirality : 0.042 0.234 1425 Planarity : 0.004 0.060 1558 Dihedral : 4.297 57.709 1243 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.96 % Allowed : 15.82 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1131 helix: 2.74 (0.27), residues: 381 sheet: 0.67 (0.31), residues: 292 loop : -1.05 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 218 TYR 0.011 0.001 TYR S 190 PHE 0.009 0.001 PHE C 189 TRP 0.012 0.001 TRP S 47 HIS 0.003 0.000 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 9115) covalent geometry : angle 0.58329 / 0.30 (12360) SS BOND : bond 0.00448 / 0.23 ( 3) SS BOND : angle 0.83025 / 0.43 ( 6) hydrogen bonds : bond 0.03304 / 2.21 ( 433) hydrogen bonds : angle 3.81968 / 2.73 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.09 seconds wall clock time: 61 minutes 5.28 seconds (3665.28 seconds total)