Starting phenix.real_space_refine on Wed Sep 17 12:29:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y89_33682/09_2025/7y89_33682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y89_33682/09_2025/7y89_33682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y89_33682/09_2025/7y89_33682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y89_33682/09_2025/7y89_33682.map" model { file = "/net/cci-nas-00/data/ceres_data/7y89_33682/09_2025/7y89_33682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y89_33682/09_2025/7y89_33682.cif" } resolution = 3.02 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= 0.018 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 61 5.16 5 C 5506 2.51 5 N 1490 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8641 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1639 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 205} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2530 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 412 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} 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: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2288 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 11, 'TRANS': 275} Time building chain proxies: 2.27, per 1000 atoms: 0.26 Number of scatterers: 8641 At special positions: 0 Unit cell: (90.1, 119, 127.5, 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 61 16.00 O 1584 8.00 N 1490 7.00 C 5506 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=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 479.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 38.7% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.845A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.228A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.517A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 removed outlier: 3.713A pdb=" N SER C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.515A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.834A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 349 removed outlier: 3.796A pdb=" N VAL C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.888A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.690A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.882A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'A' and resid 55 through 87 Processing helix chain 'A' and resid 92 through 121 removed outlier: 4.499A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 112 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 128 through 162 removed outlier: 3.756A pdb=" N GLY A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.594A pdb=" N LEU A 168 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 169 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.712A pdb=" N ALA A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.643A pdb=" N TYR A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 249 removed outlier: 4.242A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Proline residue: A 232 - end of helix removed outlier: 3.607A pdb=" N TYR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 275 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.804A pdb=" N HIS A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 327 removed outlier: 3.530A pdb=" N ASN A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 332 through 339 Processing sheet with id=AA1, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.680A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 37 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 266 through 268 removed outlier: 3.501A pdb=" N HIS C 322 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.593A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.902A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.505A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.618A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.543A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234 removed outlier: 7.024A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 276 removed outlier: 4.258A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.192A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'S' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'S' and resid 45 through 46 Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.631A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.858A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 214 " --> pdb=" O GLN S 167 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1110 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: 1.34 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1541 1.32 - 1.44: 2324 1.44 - 1.57: 4872 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8824 Sorted by residual: bond pdb=" CA PHE B 335 " pdb=" C PHE B 335 " ideal model delta sigma weight residual 1.523 1.489 0.033 1.10e-02 8.26e+03 9.13e+00 bond pdb=" N GLU C 318 " pdb=" CA GLU C 318 " ideal model delta sigma weight residual 1.456 1.421 0.035 1.21e-02 6.83e+03 8.50e+00 bond pdb=" C GLN S 171 " pdb=" N SER S 172 " ideal model delta sigma weight residual 1.333 1.264 0.068 2.74e-02 1.33e+03 6.24e+00 bond pdb=" CA ARG A 214 " pdb=" C ARG A 214 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.34e-02 5.57e+03 5.60e+00 bond pdb=" C VAL A 207 " pdb=" O VAL A 207 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.47e-02 4.63e+03 5.33e+00 ... (remaining 8819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 11525 1.77 - 3.54: 362 3.54 - 5.31: 53 5.31 - 7.08: 11 7.08 - 8.85: 3 Bond angle restraints: 11954 Sorted by residual: angle pdb=" CA VAL A 207 " pdb=" C VAL A 207 " pdb=" O VAL A 207 " ideal model delta sigma weight residual 119.91 113.77 6.14 9.90e-01 1.02e+00 3.85e+01 angle pdb=" N CYS C 351 " pdb=" CA CYS C 351 " pdb=" C CYS C 351 " ideal model delta sigma weight residual 112.88 105.93 6.95 1.29e+00 6.01e-01 2.90e+01 angle pdb=" C VAL A 207 " pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta sigma weight residual 121.97 130.82 -8.85 1.80e+00 3.09e-01 2.42e+01 angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 110.07 104.82 5.25 1.26e+00 6.30e-01 1.74e+01 angle pdb=" N SER S 142 " pdb=" CA SER S 142 " pdb=" C SER S 142 " ideal model delta sigma weight residual 110.91 115.65 -4.74 1.17e+00 7.31e-01 1.64e+01 ... (remaining 11949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4669 17.53 - 35.06: 449 35.06 - 52.60: 84 52.60 - 70.13: 15 70.13 - 87.66: 9 Dihedral angle restraints: 5226 sinusoidal: 2005 harmonic: 3221 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+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 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA HIS A 220 " pdb=" C HIS A 220 " pdb=" N ALA A 221 " pdb=" CA ALA A 221 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 902 0.042 - 0.084: 345 0.084 - 0.126: 106 0.126 - 0.168: 10 0.168 - 0.211: 2 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA CYS A 239 " pdb=" N CYS A 239 " pdb=" C CYS A 239 " pdb=" CB CYS A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TYR A 240 " pdb=" N TYR A 240 " pdb=" C TYR A 240 " pdb=" CB TYR A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU B 14 " pdb=" CB LEU B 14 " pdb=" CD1 LEU B 14 " pdb=" CD2 LEU B 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1362 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 333 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ASP B 333 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP B 333 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 334 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 219 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C HIS A 219 " 0.046 2.00e-02 2.50e+03 pdb=" O HIS A 219 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 220 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 141 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C LEU A 141 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU A 141 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 142 " -0.015 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 167 2.65 - 3.22: 8259 3.22 - 3.78: 12896 3.78 - 4.34: 17455 4.34 - 4.90: 29698 Nonbonded interactions: 68475 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.092 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.133 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.149 3.040 nonbonded pdb=" OE2 GLU A 215 " pdb=" OH TYR A 286 " model vdw 2.163 3.040 nonbonded pdb=" O ASP C 315 " pdb=" OG1 THR C 316 " model vdw 2.195 3.040 ... (remaining 68470 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: 2.670 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 0.068 8827 Z= 0.311 Angle : 0.760 8.851 11960 Z= 0.442 Chirality : 0.047 0.211 1365 Planarity : 0.004 0.057 1508 Dihedral : 14.487 87.661 3137 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.17 % Favored : 91.47 % Rotamer: Outliers : 1.29 % Allowed : 1.61 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.26), residues: 1090 helix: 1.08 (0.28), residues: 365 sheet: -1.92 (0.30), residues: 288 loop : -1.88 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 313 TYR 0.017 0.002 TYR B 105 PHE 0.024 0.002 PHE A 139 TRP 0.015 0.002 TRP C 258 HIS 0.010 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 8824) covalent geometry : angle 0.75960 (11954) SS BOND : bond 0.00597 ( 3) SS BOND : angle 1.43676 ( 6) hydrogen bonds : bond 0.18662 ( 403) hydrogen bonds : angle 6.85991 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.356 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: C 29 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7335 (tppt) REVERT: C 276 GLU cc_start: 0.8461 (mp0) cc_final: 0.8121 (mp0) REVERT: B 268 ASN cc_start: 0.8714 (m-40) cc_final: 0.7988 (t0) REVERT: B 331 SER cc_start: 0.8621 (p) cc_final: 0.8353 (p) REVERT: A 65 PHE cc_start: 0.9071 (t80) cc_final: 0.8855 (t80) REVERT: A 86 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8075 (ttm-80) outliers start: 12 outliers final: 5 residues processed: 166 average time/residue: 0.1214 time to fit residues: 26.4530 Evaluate side-chains 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 308 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN G 11 GLN S 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090441 restraints weight = 12582.786| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.25 r_work: 0.2957 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8827 Z= 0.137 Angle : 0.597 6.799 11960 Z= 0.315 Chirality : 0.042 0.151 1365 Planarity : 0.004 0.055 1508 Dihedral : 5.895 75.318 1213 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 1.50 % Allowed : 9.02 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.26), residues: 1090 helix: 1.56 (0.28), residues: 366 sheet: -1.51 (0.31), residues: 288 loop : -1.83 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.015 0.001 TYR S 178 PHE 0.020 0.001 PHE A 65 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8824) covalent geometry : angle 0.59672 (11954) SS BOND : bond 0.00383 ( 3) SS BOND : angle 1.07194 ( 6) hydrogen bonds : bond 0.04310 ( 403) hydrogen bonds : angle 4.73556 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.346 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: symmetry clash REVERT: C 29 LYS cc_start: 0.7207 (tmtt) cc_final: 0.6767 (tppt) REVERT: C 276 GLU cc_start: 0.8548 (mp0) cc_final: 0.8060 (mp0) REVERT: C 315 ASP cc_start: 0.7946 (t0) cc_final: 0.7717 (t0) REVERT: S 76 LYS cc_start: 0.8237 (mtmt) cc_final: 0.8006 (mtmm) REVERT: S 90 ASP cc_start: 0.7817 (m-30) cc_final: 0.7550 (m-30) REVERT: S 206 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7936 (mmp80) REVERT: A 86 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8237 (ttm-80) REVERT: A 215 GLU cc_start: 0.8304 (tp30) cc_final: 0.8029 (tp30) outliers start: 14 outliers final: 7 residues processed: 166 average time/residue: 0.1163 time to fit residues: 25.4189 Evaluate side-chains 137 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 73 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN G 11 GLN S 167 GLN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092392 restraints weight = 12495.420| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.27 r_work: 0.2990 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8827 Z= 0.115 Angle : 0.550 6.689 11960 Z= 0.289 Chirality : 0.041 0.146 1365 Planarity : 0.004 0.054 1508 Dihedral : 5.256 73.041 1210 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 2.15 % Allowed : 11.60 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.26), residues: 1090 helix: 1.90 (0.28), residues: 366 sheet: -1.27 (0.31), residues: 276 loop : -1.73 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.014 0.001 TYR S 178 PHE 0.018 0.001 PHE A 65 TRP 0.009 0.001 TRP A 184 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8824) covalent geometry : angle 0.54925 (11954) SS BOND : bond 0.00390 ( 3) SS BOND : angle 1.01422 ( 6) hydrogen bonds : bond 0.03699 ( 403) hydrogen bonds : angle 4.34478 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.350 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: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7261 (tmtt) cc_final: 0.6832 (tppt) REVERT: C 276 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: B 268 ASN cc_start: 0.8844 (m-40) cc_final: 0.7987 (t0) REVERT: G 58 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: S 30 SER cc_start: 0.9224 (m) cc_final: 0.8978 (t) REVERT: S 93 MET cc_start: 0.7294 (ttm) cc_final: 0.7013 (tpp) REVERT: S 206 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7900 (mmp80) REVERT: A 86 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8221 (ttm-80) REVERT: A 215 GLU cc_start: 0.8285 (tp30) cc_final: 0.8062 (tp30) REVERT: A 249 GLN cc_start: 0.8234 (pt0) cc_final: 0.7800 (tm-30) outliers start: 20 outliers final: 9 residues processed: 158 average time/residue: 0.1245 time to fit residues: 25.7013 Evaluate side-chains 144 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN G 11 GLN S 167 GLN A 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090251 restraints weight = 12728.612| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.27 r_work: 0.2959 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8827 Z= 0.149 Angle : 0.564 6.638 11960 Z= 0.296 Chirality : 0.042 0.143 1365 Planarity : 0.004 0.052 1508 Dihedral : 5.219 69.802 1210 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 2.26 % Allowed : 13.86 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.26), residues: 1090 helix: 2.03 (0.28), residues: 365 sheet: -1.38 (0.31), residues: 286 loop : -1.65 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.013 0.001 TYR S 178 PHE 0.013 0.001 PHE S 27 TRP 0.015 0.001 TRP B 82 HIS 0.009 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8824) covalent geometry : angle 0.56374 (11954) SS BOND : bond 0.00498 ( 3) SS BOND : angle 1.03074 ( 6) hydrogen bonds : bond 0.03856 ( 403) hydrogen bonds : angle 4.26115 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.350 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: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7321 (tmtt) cc_final: 0.6844 (tppt) REVERT: C 276 GLU cc_start: 0.8519 (mp0) cc_final: 0.8043 (mp0) REVERT: B 268 ASN cc_start: 0.8872 (m-40) cc_final: 0.8027 (t0) REVERT: B 334 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7936 (m) REVERT: G 58 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: S 30 SER cc_start: 0.9210 (m) cc_final: 0.8980 (t) REVERT: S 93 MET cc_start: 0.7310 (ttm) cc_final: 0.7046 (tpp) REVERT: S 206 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7991 (mmp80) REVERT: A 86 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8217 (ttm-80) REVERT: A 191 MET cc_start: 0.7893 (mmt) cc_final: 0.7598 (mmt) REVERT: A 249 GLN cc_start: 0.8175 (pt0) cc_final: 0.7842 (tm-30) outliers start: 21 outliers final: 15 residues processed: 157 average time/residue: 0.1260 time to fit residues: 25.6579 Evaluate side-chains 153 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 39 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 11 GLN S 167 GLN A 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.088740 restraints weight = 12762.712| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.27 r_work: 0.2939 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8827 Z= 0.168 Angle : 0.571 6.565 11960 Z= 0.300 Chirality : 0.042 0.138 1365 Planarity : 0.004 0.052 1508 Dihedral : 5.241 66.151 1210 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 2.47 % Allowed : 14.72 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.26), residues: 1090 helix: 2.03 (0.28), residues: 365 sheet: -1.36 (0.31), residues: 282 loop : -1.66 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.013 0.001 TYR S 178 PHE 0.014 0.002 PHE S 27 TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8824) covalent geometry : angle 0.57078 (11954) SS BOND : bond 0.00548 ( 3) SS BOND : angle 1.17601 ( 6) hydrogen bonds : bond 0.03950 ( 403) hydrogen bonds : angle 4.26084 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.353 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: symmetry clash REVERT: C 29 LYS cc_start: 0.7308 (tmtt) cc_final: 0.6817 (tppt) REVERT: C 273 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8944 (tt) REVERT: C 276 GLU cc_start: 0.8517 (mp0) cc_final: 0.8034 (mp0) REVERT: B 234 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: B 268 ASN cc_start: 0.8863 (m-40) cc_final: 0.7989 (t0) REVERT: B 334 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7982 (m) REVERT: G 58 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: S 30 SER cc_start: 0.9187 (m) cc_final: 0.8971 (t) REVERT: S 206 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7961 (mmp80) REVERT: A 86 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8209 (ttm-80) REVERT: A 214 ARG cc_start: 0.6737 (mmm160) cc_final: 0.6060 (mmm160) REVERT: A 215 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 249 GLN cc_start: 0.8049 (pt0) cc_final: 0.7761 (tm-30) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 0.1237 time to fit residues: 24.7209 Evaluate side-chains 149 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.0570 chunk 98 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN G 11 GLN A 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092008 restraints weight = 12637.426| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.28 r_work: 0.2987 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8827 Z= 0.110 Angle : 0.531 6.474 11960 Z= 0.277 Chirality : 0.041 0.138 1365 Planarity : 0.003 0.050 1508 Dihedral : 5.047 62.599 1210 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 2.90 % Allowed : 15.15 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.26), residues: 1090 helix: 2.24 (0.28), residues: 366 sheet: -1.09 (0.31), residues: 272 loop : -1.62 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.014 0.001 TYR S 178 PHE 0.014 0.001 PHE A 127 TRP 0.014 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8824) covalent geometry : angle 0.53033 (11954) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.85407 ( 6) hydrogen bonds : bond 0.03392 ( 403) hydrogen bonds : angle 4.05821 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.414 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: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7268 (tmtt) cc_final: 0.6836 (tppt) REVERT: C 242 ARG cc_start: 0.7760 (mtm180) cc_final: 0.7337 (mtm180) REVERT: C 315 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7832 (t0) REVERT: B 268 ASN cc_start: 0.8849 (m-40) cc_final: 0.7965 (t0) REVERT: B 334 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7907 (m) REVERT: G 58 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: S 91 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8098 (m) REVERT: S 206 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7909 (mmp80) REVERT: A 86 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8222 (ttm-80) REVERT: A 214 ARG cc_start: 0.6801 (mmm160) cc_final: 0.6275 (mmm160) outliers start: 27 outliers final: 16 residues processed: 157 average time/residue: 0.1203 time to fit residues: 24.8510 Evaluate side-chains 153 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN B 17 GLN G 11 GLN A 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091676 restraints weight = 12701.310| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.28 r_work: 0.2986 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8827 Z= 0.124 Angle : 0.558 8.314 11960 Z= 0.287 Chirality : 0.041 0.138 1365 Planarity : 0.003 0.049 1508 Dihedral : 5.060 58.983 1210 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 2.69 % Allowed : 16.22 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.26), residues: 1090 helix: 2.34 (0.28), residues: 365 sheet: -1.06 (0.31), residues: 272 loop : -1.52 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.013 0.001 TYR S 178 PHE 0.011 0.001 PHE A 127 TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8824) covalent geometry : angle 0.55776 (11954) SS BOND : bond 0.00425 ( 3) SS BOND : angle 1.02459 ( 6) hydrogen bonds : bond 0.03457 ( 403) hydrogen bonds : angle 4.04573 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 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: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7329 (tmtt) cc_final: 0.6884 (tppt) REVERT: C 242 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7402 (mtm180) REVERT: C 276 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8144 (mt-10) REVERT: C 315 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7839 (t0) REVERT: B 268 ASN cc_start: 0.8840 (m-40) cc_final: 0.7963 (t0) REVERT: B 334 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7894 (m) REVERT: G 58 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: S 91 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 86 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8220 (ttm-80) REVERT: A 214 ARG cc_start: 0.6775 (mmm160) cc_final: 0.6147 (mmm160) REVERT: A 215 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7822 (mm-30) outliers start: 25 outliers final: 16 residues processed: 157 average time/residue: 0.1225 time to fit residues: 25.2106 Evaluate side-chains 155 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.0000 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 11 GLN A 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092268 restraints weight = 12587.265| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.28 r_work: 0.2999 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8827 Z= 0.113 Angle : 0.552 7.421 11960 Z= 0.285 Chirality : 0.041 0.132 1365 Planarity : 0.003 0.047 1508 Dihedral : 4.985 55.122 1210 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 2.90 % Allowed : 16.54 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.26), residues: 1090 helix: 2.39 (0.28), residues: 365 sheet: -1.03 (0.31), residues: 274 loop : -1.47 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 313 TYR 0.013 0.001 TYR S 178 PHE 0.025 0.001 PHE A 182 TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8824) covalent geometry : angle 0.55195 (11954) SS BOND : bond 0.00379 ( 3) SS BOND : angle 0.86227 ( 6) hydrogen bonds : bond 0.03297 ( 403) hydrogen bonds : angle 3.96495 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.356 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: symmetry clash REVERT: C 29 LYS cc_start: 0.7267 (tmtt) cc_final: 0.6821 (tppt) REVERT: C 276 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8233 (mt-10) REVERT: C 315 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7813 (t0) REVERT: B 334 SER cc_start: 0.8130 (OUTLIER) cc_final: 0.7860 (m) REVERT: S 91 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8100 (p) REVERT: S 206 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7586 (mmm160) REVERT: A 86 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8220 (ttm-80) REVERT: A 191 MET cc_start: 0.7647 (mmt) cc_final: 0.7387 (mmm) REVERT: A 214 ARG cc_start: 0.6731 (mmm160) cc_final: 0.6127 (mmm160) REVERT: A 215 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7846 (mm-30) outliers start: 27 outliers final: 18 residues processed: 153 average time/residue: 0.1161 time to fit residues: 23.3995 Evaluate side-chains 152 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN G 11 GLN A 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090785 restraints weight = 12562.593| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.27 r_work: 0.2977 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8827 Z= 0.143 Angle : 0.583 7.205 11960 Z= 0.301 Chirality : 0.042 0.151 1365 Planarity : 0.003 0.048 1508 Dihedral : 5.020 54.442 1210 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 2.58 % Allowed : 17.29 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1090 helix: 2.39 (0.28), residues: 364 sheet: -1.11 (0.31), residues: 282 loop : -1.45 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 313 TYR 0.013 0.001 TYR B 59 PHE 0.025 0.002 PHE A 182 TRP 0.016 0.001 TRP C 258 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8824) covalent geometry : angle 0.58233 (11954) SS BOND : bond 0.00460 ( 3) SS BOND : angle 1.11590 ( 6) hydrogen bonds : bond 0.03537 ( 403) hydrogen bonds : angle 3.99354 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 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: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7301 (tmtt) cc_final: 0.6847 (tppt) REVERT: C 276 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8255 (mt-10) REVERT: C 315 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7818 (t0) REVERT: B 254 ASP cc_start: 0.8291 (t0) cc_final: 0.8047 (t0) REVERT: B 268 ASN cc_start: 0.8796 (m-40) cc_final: 0.7893 (t0) REVERT: B 334 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7914 (m) REVERT: S 91 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8060 (p) REVERT: S 206 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7828 (mmp80) REVERT: A 86 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8218 (ttm-80) REVERT: A 191 MET cc_start: 0.7702 (mmt) cc_final: 0.7474 (mmm) REVERT: A 214 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6116 (mmm160) REVERT: A 215 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7883 (mm-30) outliers start: 24 outliers final: 19 residues processed: 151 average time/residue: 0.1160 time to fit residues: 23.1822 Evaluate side-chains 153 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 8 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN B 17 GLN B 340 ASN G 11 GLN A 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093108 restraints weight = 12662.316| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.30 r_work: 0.3014 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8827 Z= 0.107 Angle : 0.556 7.180 11960 Z= 0.287 Chirality : 0.041 0.134 1365 Planarity : 0.003 0.048 1508 Dihedral : 4.880 54.402 1210 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 17.29 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.26), residues: 1090 helix: 2.47 (0.28), residues: 364 sheet: -0.95 (0.31), residues: 274 loop : -1.41 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 313 TYR 0.013 0.001 TYR S 178 PHE 0.026 0.001 PHE A 182 TRP 0.014 0.001 TRP A 184 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8824) covalent geometry : angle 0.55596 (11954) SS BOND : bond 0.00349 ( 3) SS BOND : angle 0.83969 ( 6) hydrogen bonds : bond 0.03188 ( 403) hydrogen bonds : angle 3.92048 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.358 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: symmetry clash REVERT: C 29 LYS cc_start: 0.7213 (tmtt) cc_final: 0.6772 (tppt) REVERT: C 276 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8248 (mt-10) REVERT: C 315 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7808 (t0) REVERT: B 254 ASP cc_start: 0.8176 (t0) cc_final: 0.7926 (t0) REVERT: B 291 ASP cc_start: 0.8274 (m-30) cc_final: 0.7934 (m-30) REVERT: B 334 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7821 (m) REVERT: S 91 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8063 (p) REVERT: S 93 MET cc_start: 0.7261 (ttm) cc_final: 0.7005 (tpp) REVERT: S 206 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7785 (mmm160) REVERT: A 86 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8179 (ttm-80) REVERT: A 191 MET cc_start: 0.7668 (mmt) cc_final: 0.7417 (mmm) outliers start: 25 outliers final: 16 residues processed: 155 average time/residue: 0.1255 time to fit residues: 25.2952 Evaluate side-chains 151 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 chunk 91 optimal weight: 0.0060 chunk 27 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN G 11 GLN S 82 GLN A 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094364 restraints weight = 12514.025| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.29 r_work: 0.3025 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8827 Z= 0.109 Angle : 0.574 7.049 11960 Z= 0.295 Chirality : 0.041 0.134 1365 Planarity : 0.003 0.048 1508 Dihedral : 4.828 53.602 1210 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 2.58 % Allowed : 17.72 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 1090 helix: 2.52 (0.27), residues: 364 sheet: -0.89 (0.31), residues: 276 loop : -1.34 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 313 TYR 0.013 0.001 TYR S 178 PHE 0.028 0.001 PHE A 182 TRP 0.016 0.001 TRP C 258 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8824) covalent geometry : angle 0.57404 (11954) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.90886 ( 6) hydrogen bonds : bond 0.03117 ( 403) hydrogen bonds : angle 3.84285 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.24 seconds wall clock time: 43 minutes 24.74 seconds (2604.74 seconds total)