Starting phenix.real_space_refine on Sat Jul 26 15:12:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y89_33682/07_2025/7y89_33682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y89_33682/07_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_33682/07_2025/7y89_33682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y89_33682/07_2025/7y89_33682.map" model { file = "/net/cci-nas-00/data/ceres_data/7y89_33682/07_2025/7y89_33682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y89_33682/07_2025/7y89_33682.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ASP:plan': 3} 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: 5.79, per 1000 atoms: 0.67 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.12 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: 2.57 Time building geometry restraints manager: 2.73 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- 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 : 11.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (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 TRP 0.015 0.002 TRP C 258 HIS 0.010 0.001 HIS B 183 PHE 0.024 0.002 PHE A 139 TYR 0.017 0.002 TYR B 105 ARG 0.008 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.18662 ( 403) hydrogen bonds : angle 6.85991 ( 1110) SS BOND : bond 0.00597 ( 3) SS BOND : angle 1.43676 ( 6) covalent geometry : bond 0.00698 ( 8824) covalent geometry : angle 0.75960 (11954) *********************** 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 : 1.005 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: 0.2585 time to fit residues: 56.3302 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 : 0.973 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091134 restraints weight = 12479.285| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.24 r_work: 0.2969 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8827 Z= 0.129 Angle : 0.592 6.783 11960 Z= 0.312 Chirality : 0.042 0.153 1365 Planarity : 0.004 0.055 1508 Dihedral : 5.878 75.398 1213 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1090 helix: 1.59 (0.28), residues: 366 sheet: -1.49 (0.31), residues: 288 loop : -1.81 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS A 205 PHE 0.019 0.001 PHE A 65 TYR 0.015 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 403) hydrogen bonds : angle 4.70284 ( 1110) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.04310 ( 6) covalent geometry : bond 0.00280 ( 8824) covalent geometry : angle 0.59134 (11954) *********************** 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 173 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.949 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: 0.7199 (tmtt) cc_final: 0.6761 (tppt) REVERT: C 276 GLU cc_start: 0.8533 (mp0) cc_final: 0.8105 (mp0) REVERT: C 315 ASP cc_start: 0.7934 (t0) cc_final: 0.7701 (t0) REVERT: S 76 LYS cc_start: 0.8243 (mtmt) cc_final: 0.8012 (mtmm) REVERT: S 90 ASP cc_start: 0.7801 (m-30) cc_final: 0.7569 (m-30) REVERT: S 206 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7959 (mmp80) REVERT: A 86 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8250 (ttm-80) REVERT: A 215 GLU cc_start: 0.8314 (tp30) cc_final: 0.8039 (tp30) outliers start: 14 outliers final: 7 residues processed: 169 average time/residue: 0.2594 time to fit residues: 57.8605 Evaluate side-chains 139 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 45 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 27 optimal weight: 0.0270 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.137338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091347 restraints weight = 12606.859| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.28 r_work: 0.2982 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8827 Z= 0.119 Angle : 0.554 6.699 11960 Z= 0.291 Chirality : 0.041 0.147 1365 Planarity : 0.004 0.054 1508 Dihedral : 5.267 72.934 1210 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.06 % Favored : 93.85 % Rotamer: Outliers : 2.15 % Allowed : 11.49 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1090 helix: 1.89 (0.28), residues: 366 sheet: -1.30 (0.31), residues: 283 loop : -1.73 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.019 0.001 PHE A 65 TYR 0.014 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 403) hydrogen bonds : angle 4.34402 ( 1110) SS BOND : bond 0.00414 ( 3) SS BOND : angle 1.04831 ( 6) covalent geometry : bond 0.00264 ( 8824) covalent geometry : angle 0.55394 (11954) *********************** 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 : 1.043 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: 0.7257 (tmtt) cc_final: 0.6822 (tppt) REVERT: C 276 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: B 268 ASN cc_start: 0.8874 (m-40) cc_final: 0.7984 (t0) REVERT: G 58 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: S 19 LYS cc_start: 0.7291 (tmtt) cc_final: 0.7087 (tmtt) REVERT: S 30 SER cc_start: 0.9215 (m) cc_final: 0.8981 (t) REVERT: S 93 MET cc_start: 0.7236 (ttm) cc_final: 0.6961 (tpp) REVERT: S 206 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7898 (mmp80) REVERT: A 86 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8216 (ttm-80) REVERT: A 215 GLU cc_start: 0.8301 (tp30) cc_final: 0.8075 (tp30) REVERT: A 249 GLN cc_start: 0.8226 (pt0) cc_final: 0.7795 (tm-30) outliers start: 20 outliers final: 9 residues processed: 159 average time/residue: 0.2621 time to fit residues: 54.8208 Evaluate side-chains 146 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 53 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN A 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089242 restraints weight = 12681.267| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.27 r_work: 0.2952 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8827 Z= 0.159 Angle : 0.570 6.636 11960 Z= 0.300 Chirality : 0.042 0.143 1365 Planarity : 0.004 0.052 1508 Dihedral : 5.243 69.462 1210 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.06 % Favored : 93.85 % Rotamer: Outliers : 2.04 % Allowed : 13.96 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1090 helix: 1.98 (0.28), residues: 365 sheet: -1.32 (0.31), residues: 287 loop : -1.68 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS A 205 PHE 0.014 0.001 PHE S 27 TYR 0.013 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 403) hydrogen bonds : angle 4.27905 ( 1110) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.07172 ( 6) covalent geometry : bond 0.00378 ( 8824) covalent geometry : angle 0.57003 (11954) *********************** 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 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.022 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: 0.7336 (tmtt) cc_final: 0.6851 (tppt) REVERT: C 276 GLU cc_start: 0.8529 (mp0) cc_final: 0.8048 (mp0) REVERT: B 268 ASN cc_start: 0.8877 (m-40) cc_final: 0.8028 (t0) REVERT: B 334 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7949 (m) REVERT: G 58 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: S 30 SER cc_start: 0.9209 (m) cc_final: 0.8983 (t) REVERT: S 82 GLN cc_start: 0.7527 (tp-100) cc_final: 0.7200 (tp-100) REVERT: S 206 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7997 (mmp80) REVERT: A 86 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8241 (ttm-80) REVERT: A 249 GLN cc_start: 0.8164 (pt0) cc_final: 0.7836 (tm-30) outliers start: 19 outliers final: 14 residues processed: 150 average time/residue: 0.2581 time to fit residues: 50.6720 Evaluate side-chains 149 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 84 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.137989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092359 restraints weight = 12557.447| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.27 r_work: 0.2989 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8827 Z= 0.112 Angle : 0.532 6.536 11960 Z= 0.279 Chirality : 0.041 0.137 1365 Planarity : 0.003 0.051 1508 Dihedral : 5.080 66.275 1210 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 2.36 % Allowed : 14.07 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1090 helix: 2.16 (0.28), residues: 365 sheet: -1.15 (0.31), residues: 274 loop : -1.62 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 PHE 0.014 0.001 PHE A 127 TYR 0.013 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 403) hydrogen bonds : angle 4.11420 ( 1110) SS BOND : bond 0.00407 ( 3) SS BOND : angle 0.93694 ( 6) covalent geometry : bond 0.00249 ( 8824) covalent geometry : angle 0.53147 (11954) *********************** 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 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.015 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: 0.7218 (tmtt) cc_final: 0.6797 (tppt) REVERT: B 268 ASN cc_start: 0.8843 (m-40) cc_final: 0.7962 (t0) REVERT: B 334 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7871 (m) REVERT: G 58 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: S 30 SER cc_start: 0.9210 (m) cc_final: 0.8983 (t) REVERT: S 82 GLN cc_start: 0.7450 (tp-100) cc_final: 0.7117 (tp-100) REVERT: S 206 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7980 (mmp80) REVERT: A 86 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8227 (ttm-80) REVERT: A 214 ARG cc_start: 0.6765 (mmm160) cc_final: 0.6123 (mmm160) REVERT: A 215 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7848 (mm-30) outliers start: 22 outliers final: 14 residues processed: 160 average time/residue: 0.2614 time to fit residues: 54.9442 Evaluate side-chains 153 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3698 r_free = 0.3698 target = 0.132716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.086811 restraints weight = 12606.651| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.25 r_work: 0.2914 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8827 Z= 0.233 Angle : 0.627 6.803 11960 Z= 0.328 Chirality : 0.044 0.143 1365 Planarity : 0.004 0.051 1508 Dihedral : 5.345 62.339 1210 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 3.11 % Allowed : 15.90 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1090 helix: 1.95 (0.27), residues: 365 sheet: -1.37 (0.31), residues: 281 loop : -1.61 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 258 HIS 0.008 0.001 HIS B 183 PHE 0.018 0.002 PHE S 27 TYR 0.016 0.002 TYR B 59 ARG 0.004 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 403) hydrogen bonds : angle 4.34874 ( 1110) SS BOND : bond 0.00639 ( 3) SS BOND : angle 1.39599 ( 6) covalent geometry : bond 0.00561 ( 8824) covalent geometry : angle 0.62601 (11954) *********************** 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 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.019 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: 0.7420 (tmtt) cc_final: 0.6908 (tppt) REVERT: C 276 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8026 (mp0) REVERT: C 315 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 42 ARG cc_start: 0.7948 (tmt170) cc_final: 0.7736 (tmt170) REVERT: B 268 ASN cc_start: 0.8878 (m-40) cc_final: 0.7978 (t0) REVERT: B 334 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8093 (m) REVERT: G 58 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: S 30 SER cc_start: 0.9172 (m) cc_final: 0.8963 (t) REVERT: S 90 ASP cc_start: 0.7749 (m-30) cc_final: 0.7402 (m-30) REVERT: S 91 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8266 (m) REVERT: S 206 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7879 (mmp80) REVERT: A 86 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8207 (ttm-80) REVERT: A 214 ARG cc_start: 0.6766 (mmm160) cc_final: 0.6060 (mmm160) REVERT: A 215 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7810 (mm-30) outliers start: 29 outliers final: 17 residues processed: 156 average time/residue: 0.2591 time to fit residues: 52.9331 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 : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 181 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 111 VAL 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 83 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 47 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3772 r_free = 0.3772 target = 0.138718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093037 restraints weight = 12684.181| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.30 r_work: 0.3001 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8827 Z= 0.102 Angle : 0.538 7.515 11960 Z= 0.279 Chirality : 0.040 0.136 1365 Planarity : 0.003 0.049 1508 Dihedral : 5.034 57.893 1210 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 2.47 % Allowed : 16.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1090 helix: 2.35 (0.28), residues: 364 sheet: -1.08 (0.31), residues: 272 loop : -1.52 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 184 HIS 0.008 0.001 HIS A 205 PHE 0.010 0.001 PHE C 189 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 403) hydrogen bonds : angle 4.02426 ( 1110) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.79738 ( 6) covalent geometry : bond 0.00214 ( 8824) covalent geometry : angle 0.53814 (11954) *********************** 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 166 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.084 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: 0.7233 (tmtt) cc_final: 0.6790 (tppt) REVERT: C 276 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8236 (mt-10) REVERT: C 315 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7815 (t0) REVERT: B 268 ASN cc_start: 0.8774 (m-40) cc_final: 0.7871 (t0) REVERT: B 334 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7836 (m) REVERT: S 82 GLN cc_start: 0.7403 (tp-100) cc_final: 0.7057 (tp-100) REVERT: S 91 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8233 (m) REVERT: S 93 MET cc_start: 0.7307 (ttm) cc_final: 0.7060 (tpp) REVERT: S 206 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7947 (mmp80) REVERT: A 86 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8221 (ttm-80) REVERT: A 214 ARG cc_start: 0.6760 (mmm160) cc_final: 0.6125 (mmm160) REVERT: A 215 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7821 (mm-30) outliers start: 23 outliers final: 12 residues processed: 159 average time/residue: 0.2666 time to fit residues: 55.4728 Evaluate side-chains 151 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 354 PHE 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 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 181 SER 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 91 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 36 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3727 r_free = 0.3727 target = 0.135154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.089072 restraints weight = 12798.747| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.29 r_work: 0.2950 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.004 0.037 8827 Z= 0.174 Angle : 0.586 6.980 11960 Z= 0.305 Chirality : 0.042 0.149 1365 Planarity : 0.004 0.049 1508 Dihedral : 5.104 54.370 1210 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 3.11 % Allowed : 15.90 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1090 helix: 2.29 (0.28), residues: 364 sheet: -1.25 (0.30), residues: 286 loop : -1.47 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 184 HIS 0.008 0.001 HIS A 205 PHE 0.027 0.002 PHE A 182 TYR 0.014 0.001 TYR B 264 ARG 0.004 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 403) hydrogen bonds : angle 4.12247 ( 1110) SS BOND : bond 0.00515 ( 3) SS BOND : angle 1.23417 ( 6) covalent geometry : bond 0.00415 ( 8824) covalent geometry : angle 0.58576 (11954) *********************** 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 164 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.042 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: 0.7319 (tmtt) cc_final: 0.6844 (tppt) REVERT: C 276 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 315 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7803 (t0) REVERT: B 254 ASP cc_start: 0.8327 (t0) cc_final: 0.8041 (t0) REVERT: B 268 ASN cc_start: 0.8846 (m-40) cc_final: 0.7968 (t0) REVERT: B 334 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8003 (m) REVERT: S 91 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8216 (m) REVERT: S 93 MET cc_start: 0.7301 (ttm) cc_final: 0.7062 (tpp) REVERT: S 206 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7840 (mmp80) REVERT: A 86 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8215 (ttm-80) outliers start: 29 outliers final: 22 residues processed: 156 average time/residue: 0.2524 time to fit residues: 52.1515 Evaluate side-chains 158 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 188 MET 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 143 VAL Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 185 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.137071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091360 restraints weight = 12608.181| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.29 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: 0.7860 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8827 Z= 0.122 Angle : 0.568 6.892 11960 Z= 0.293 Chirality : 0.041 0.134 1365 Planarity : 0.003 0.049 1508 Dihedral : 4.984 53.033 1210 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 2.90 % Allowed : 16.11 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1090 helix: 2.42 (0.28), residues: 364 sheet: -1.06 (0.31), residues: 274 loop : -1.47 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 184 HIS 0.007 0.001 HIS A 205 PHE 0.026 0.001 PHE A 182 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 403) hydrogen bonds : angle 4.01164 ( 1110) SS BOND : bond 0.00419 ( 3) SS BOND : angle 0.92107 ( 6) covalent geometry : bond 0.00277 ( 8824) covalent geometry : angle 0.56762 (11954) *********************** 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 164 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.017 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: 0.7312 (tmtt) cc_final: 0.6858 (tppt) REVERT: C 276 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 315 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7806 (t0) REVERT: B 254 ASP cc_start: 0.8251 (t0) cc_final: 0.7998 (t0) REVERT: B 268 ASN cc_start: 0.8788 (m-40) cc_final: 0.7863 (t0) REVERT: B 334 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7881 (m) REVERT: G 58 GLU cc_start: 0.8031 (mp0) cc_final: 0.7820 (mp0) REVERT: S 82 GLN cc_start: 0.7393 (tp-100) cc_final: 0.7036 (tp-100) REVERT: S 91 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8213 (m) REVERT: S 93 MET cc_start: 0.7285 (ttm) cc_final: 0.7043 (tpp) REVERT: S 206 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7903 (mmp80) REVERT: A 86 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8219 (ttm-80) outliers start: 27 outliers final: 20 residues processed: 156 average time/residue: 0.2474 time to fit residues: 51.5603 Evaluate side-chains 155 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 143 VAL Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 111 VAL 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 66 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 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 = 0.136328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.090604 restraints weight = 12672.643| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.28 r_work: 0.2974 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2363 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= 0.136 Angle : 0.564 7.012 11960 Z= 0.294 Chirality : 0.041 0.135 1365 Planarity : 0.003 0.048 1508 Dihedral : 4.965 53.492 1210 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 2.79 % Allowed : 16.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1090 helix: 2.42 (0.27), residues: 364 sheet: -1.15 (0.31), residues: 283 loop : -1.42 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS A 205 PHE 0.027 0.001 PHE A 182 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 403) hydrogen bonds : angle 4.01570 ( 1110) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.10469 ( 6) covalent geometry : bond 0.00318 ( 8824) covalent geometry : angle 0.56369 (11954) ********************** 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 161 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.030 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: 0.7303 (tmtt) cc_final: 0.6844 (tppt) REVERT: C 276 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8281 (mt-10) REVERT: C 313 ARG cc_start: 0.7234 (ttm-80) cc_final: 0.6968 (ttm-80) REVERT: C 315 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7784 (t0) REVERT: B 254 ASP cc_start: 0.8293 (t0) cc_final: 0.8005 (t0) REVERT: B 268 ASN cc_start: 0.8794 (m-40) cc_final: 0.7891 (t0) REVERT: B 334 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7903 (m) REVERT: G 58 GLU cc_start: 0.7986 (mp0) cc_final: 0.7780 (mp0) REVERT: S 82 GLN cc_start: 0.7379 (tp-100) cc_final: 0.6990 (tp-100) REVERT: S 91 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8154 (m) REVERT: S 93 MET cc_start: 0.7250 (ttm) cc_final: 0.7006 (tpp) REVERT: A 86 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8221 (ttm-80) outliers start: 26 outliers final: 20 residues processed: 153 average time/residue: 0.2474 time to fit residues: 51.0685 Evaluate side-chains 154 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 S residue 222 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 185 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 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 = 0.3726 r_free = 0.3726 target = 0.135041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089373 restraints weight = 12704.903| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.29 r_work: 0.2955 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8827 Z= 0.170 Angle : 0.612 10.271 11960 Z= 0.316 Chirality : 0.042 0.136 1365 Planarity : 0.003 0.048 1508 Dihedral : 5.044 56.912 1210 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 2.79 % Allowed : 16.43 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1090 helix: 2.32 (0.27), residues: 364 sheet: -1.19 (0.30), residues: 286 loop : -1.44 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 184 HIS 0.007 0.001 HIS A 205 PHE 0.028 0.002 PHE A 182 TYR 0.013 0.001 TYR B 264 ARG 0.005 0.000 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 403) hydrogen bonds : angle 4.08975 ( 1110) SS BOND : bond 0.00523 ( 3) SS BOND : angle 1.17846 ( 6) covalent geometry : bond 0.00406 ( 8824) covalent geometry : angle 0.61144 (11954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4784.87 seconds wall clock time: 82 minutes 41.39 seconds (4961.39 seconds total)