Starting phenix.real_space_refine on Sat Dec 28 14:44:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y89_33682/12_2024/7y89_33682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y89_33682/12_2024/7y89_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_33682/12_2024/7y89_33682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y89_33682/12_2024/7y89_33682.map" model { file = "/net/cci-nas-00/data/ceres_data/7y89_33682/12_2024/7y89_33682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y89_33682/12_2024/7y89_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-5532/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: 5.72, per 1000 atoms: 0.66 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 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: 1.05 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: 2.56 Time building geometry restraints manager: 2.84 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: 2.920 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: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.990 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: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- 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 8824 Z= 0.459 Angle : 0.760 8.851 11954 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 *********************** 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 : 1.004 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: 0.2699 time to fit residues: 58.4782 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 : 0.999 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 8824 Z= 0.185 Angle : 0.591 6.783 11954 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 *********************** 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 : 1.041 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: 0.7698 (tmtt) cc_final: 0.7247 (tppt) REVERT: C 276 GLU cc_start: 0.8435 (mp0) cc_final: 0.8034 (mp0) REVERT: S 76 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8093 (mtmm) REVERT: S 90 ASP cc_start: 0.7926 (m-30) cc_final: 0.7721 (m-30) REVERT: S 206 ARG cc_start: 0.8400 (mmm160) cc_final: 0.8081 (mmp80) REVERT: A 86 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8198 (ttm-80) REVERT: A 214 ARG cc_start: 0.7248 (mmm160) cc_final: 0.7039 (mmm160) outliers start: 14 outliers final: 7 residues processed: 169 average time/residue: 0.2679 time to fit residues: 59.4994 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 : 1.017 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8824 Z= 0.199 Angle : 0.565 6.686 11954 Z= 0.297 Chirality : 0.042 0.166 1365 Planarity : 0.004 0.054 1508 Dihedral : 5.311 72.719 1210 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 2.26 % Allowed : 11.49 % 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 (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: -0.63 (0.26), residues: 1090 helix: 1.85 (0.28), residues: 366 sheet: -1.38 (0.31), residues: 285 loop : -1.70 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE A 65 TYR 0.014 0.001 TYR S 178 ARG 0.003 0.000 ARG C 313 *********************** 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 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 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: C 29 LYS cc_start: 0.7705 (tmtt) cc_final: 0.7278 (tppt) REVERT: C 276 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: C 330 LYS cc_start: 0.8173 (pttm) cc_final: 0.7728 (mmtm) REVERT: B 268 ASN cc_start: 0.8681 (m-40) cc_final: 0.7957 (t0) REVERT: G 36 ASP cc_start: 0.8355 (t0) cc_final: 0.8125 (t0) REVERT: S 30 SER cc_start: 0.8815 (m) cc_final: 0.8607 (t) REVERT: S 206 ARG cc_start: 0.8390 (mmm160) cc_final: 0.8055 (mmp80) REVERT: A 86 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8160 (ttm-80) REVERT: A 249 GLN cc_start: 0.8248 (pt0) cc_final: 0.7845 (tm-30) outliers start: 21 outliers final: 9 residues processed: 159 average time/residue: 0.2648 time to fit residues: 54.8696 Evaluate side-chains 145 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 97 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 51 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8824 Z= 0.225 Angle : 0.566 6.705 11954 Z= 0.299 Chirality : 0.042 0.153 1365 Planarity : 0.004 0.052 1508 Dihedral : 5.249 69.804 1210 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 2.04 % Allowed : 13.75 % Favored : 84.21 % 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: -0.52 (0.26), residues: 1090 helix: 1.95 (0.28), residues: 366 sheet: -1.36 (0.31), residues: 291 loop : -1.60 (0.28), residues: 433 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 0.012 0.001 PHE A 65 TYR 0.014 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 *********************** 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 160 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.062 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: 0.7757 (tmtt) cc_final: 0.7314 (tppt) REVERT: C 276 GLU cc_start: 0.8423 (mp0) cc_final: 0.7961 (mp0) REVERT: B 268 ASN cc_start: 0.8656 (m-40) cc_final: 0.7952 (t0) REVERT: B 334 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7793 (m) REVERT: G 36 ASP cc_start: 0.8337 (t0) cc_final: 0.8106 (t0) REVERT: S 206 ARG cc_start: 0.8397 (mmm160) cc_final: 0.8044 (mmp80) REVERT: A 86 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8127 (ttm-80) REVERT: A 214 ARG cc_start: 0.7166 (mmm160) cc_final: 0.6369 (mmm160) REVERT: A 215 GLU cc_start: 0.8067 (tp30) cc_final: 0.7735 (tp30) REVERT: A 249 GLN cc_start: 0.8223 (pt0) cc_final: 0.7901 (tm-30) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.2582 time to fit residues: 51.6817 Evaluate side-chains 158 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** B 17 GLN G 11 GLN A 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8824 Z= 0.220 Angle : 0.551 6.566 11954 Z= 0.290 Chirality : 0.042 0.150 1365 Planarity : 0.004 0.051 1508 Dihedral : 5.170 66.483 1210 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 2.36 % Allowed : 14.29 % Favored : 83.35 % 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: -0.44 (0.26), residues: 1090 helix: 2.06 (0.28), residues: 366 sheet: -1.33 (0.31), residues: 284 loop : -1.60 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 PHE 0.027 0.001 PHE A 65 TYR 0.013 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 *********************** 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 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.076 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: 0.7759 (tmtt) cc_final: 0.7317 (tppt) REVERT: C 273 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8995 (tt) REVERT: C 276 GLU cc_start: 0.8435 (mp0) cc_final: 0.7987 (mp0) REVERT: B 234 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: B 268 ASN cc_start: 0.8667 (m-40) cc_final: 0.7958 (t0) REVERT: B 334 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7812 (m) REVERT: G 36 ASP cc_start: 0.8310 (t0) cc_final: 0.8104 (t0) REVERT: S 206 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8142 (mmp80) REVERT: A 86 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8162 (ttm-80) REVERT: A 214 ARG cc_start: 0.7060 (mmm160) cc_final: 0.6491 (mmm160) REVERT: A 215 GLU cc_start: 0.8073 (tp30) cc_final: 0.7785 (tp30) REVERT: A 249 GLN cc_start: 0.8115 (pt0) cc_final: 0.7899 (tm-30) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 0.2626 time to fit residues: 56.4216 Evaluate side-chains 148 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8824 Z= 0.147 Angle : 0.530 6.471 11954 Z= 0.277 Chirality : 0.041 0.139 1365 Planarity : 0.003 0.050 1508 Dihedral : 5.010 63.649 1210 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 3.44 % Allowed : 14.72 % Favored : 81.85 % 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: -0.21 (0.26), residues: 1090 helix: 2.26 (0.28), residues: 366 sheet: -1.06 (0.32), residues: 272 loop : -1.59 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 PHE 0.014 0.001 PHE A 127 TYR 0.014 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 *********************** 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 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.983 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: 0.7679 (tmtt) cc_final: 0.7261 (tppt) REVERT: B 268 ASN cc_start: 0.8639 (m-40) cc_final: 0.7923 (t0) REVERT: B 334 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7700 (m) REVERT: S 91 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8661 (m) REVERT: S 206 ARG cc_start: 0.8315 (mmm160) cc_final: 0.8085 (mmp80) REVERT: A 86 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8177 (ttm-80) REVERT: A 191 MET cc_start: 0.7716 (mmt) cc_final: 0.7515 (mmm) REVERT: A 214 ARG cc_start: 0.7069 (mmm160) cc_final: 0.6513 (mmm160) REVERT: A 215 GLU cc_start: 0.7971 (tp30) cc_final: 0.7655 (tp30) outliers start: 32 outliers final: 17 residues processed: 162 average time/residue: 0.2486 time to fit residues: 53.0301 Evaluate side-chains 156 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 30 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 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 11 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8824 Z= 0.309 Angle : 0.611 7.893 11954 Z= 0.318 Chirality : 0.043 0.147 1365 Planarity : 0.004 0.050 1508 Dihedral : 5.211 59.702 1210 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 2.58 % Allowed : 16.22 % Favored : 81.20 % 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: 2.13 (0.28), residues: 364 sheet: -1.22 (0.31), residues: 278 loop : -1.53 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 258 HIS 0.008 0.001 HIS A 205 PHE 0.016 0.002 PHE S 27 TYR 0.013 0.002 TYR S 178 ARG 0.004 0.000 ARG C 313 *********************** 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 173 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.071 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: 0.7781 (tmtt) cc_final: 0.7307 (tppt) REVERT: C 276 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7949 (mp0) REVERT: B 268 ASN cc_start: 0.8667 (m-40) cc_final: 0.7934 (t0) REVERT: B 334 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7913 (m) REVERT: S 90 ASP cc_start: 0.7849 (m-30) cc_final: 0.7504 (m-30) REVERT: S 91 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8592 (p) REVERT: S 206 ARG cc_start: 0.8385 (mmm160) cc_final: 0.8115 (mmp80) REVERT: A 86 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8170 (ttm-80) REVERT: A 214 ARG cc_start: 0.7075 (mmm160) cc_final: 0.6259 (mmm160) outliers start: 24 outliers final: 19 residues processed: 167 average time/residue: 0.2590 time to fit residues: 56.7008 Evaluate side-chains 154 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 30 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 273 LEU 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 62 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** G 11 GLN A 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8824 Z= 0.237 Angle : 0.582 7.375 11954 Z= 0.302 Chirality : 0.042 0.140 1365 Planarity : 0.003 0.049 1508 Dihedral : 4.892 55.330 1206 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.64 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: -0.26 (0.26), residues: 1090 helix: 2.22 (0.28), residues: 364 sheet: -1.22 (0.31), residues: 280 loop : -1.49 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 PHE 0.014 0.001 PHE S 27 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG C 313 *********************** 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 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.262 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: 0.7770 (tmtt) cc_final: 0.7314 (tppt) REVERT: C 276 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 268 ASN cc_start: 0.8665 (m-40) cc_final: 0.7926 (t0) REVERT: B 334 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7867 (m) REVERT: S 90 ASP cc_start: 0.7835 (m-30) cc_final: 0.7458 (m-30) REVERT: S 91 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8590 (p) REVERT: S 93 MET cc_start: 0.7417 (ttm) cc_final: 0.7177 (tpp) REVERT: S 206 ARG cc_start: 0.8380 (mmm160) cc_final: 0.8106 (mmp80) REVERT: A 86 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8172 (ttm-80) REVERT: A 214 ARG cc_start: 0.6735 (mmm160) cc_final: 0.6269 (mmm160) outliers start: 27 outliers final: 20 residues processed: 160 average time/residue: 0.2512 time to fit residues: 53.3192 Evaluate side-chains 159 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 30 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 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 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 97 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 92 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 103 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8824 Z= 0.168 Angle : 0.571 7.296 11954 Z= 0.296 Chirality : 0.041 0.136 1365 Planarity : 0.003 0.048 1508 Dihedral : 4.719 50.303 1206 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 2.47 % Allowed : 16.86 % Favored : 80.67 % 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: -0.09 (0.26), residues: 1090 helix: 2.35 (0.28), residues: 364 sheet: -1.03 (0.31), residues: 274 loop : -1.45 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 205 PHE 0.010 0.001 PHE A 127 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG C 313 *********************** 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 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.059 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: 0.7692 (tmtt) cc_final: 0.7263 (tppt) REVERT: C 276 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 313 ARG cc_start: 0.7188 (ttm-80) cc_final: 0.6649 (ttm-80) REVERT: B 268 ASN cc_start: 0.8634 (m-40) cc_final: 0.7860 (t0) REVERT: B 334 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7717 (m) REVERT: S 91 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8536 (p) REVERT: S 93 MET cc_start: 0.7380 (ttm) cc_final: 0.7173 (tpp) REVERT: S 206 ARG cc_start: 0.8325 (mmm160) cc_final: 0.8086 (mmp80) REVERT: A 86 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8179 (ttm-80) REVERT: A 214 ARG cc_start: 0.6641 (mmm160) cc_final: 0.6302 (mmm160) outliers start: 23 outliers final: 19 residues processed: 161 average time/residue: 0.2451 time to fit residues: 53.1698 Evaluate side-chains 159 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 30 SER Chi-restraints excluded: chain S residue 57 THR 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 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 49 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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** G 11 GLN A 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8824 Z= 0.159 Angle : 0.572 7.229 11954 Z= 0.296 Chirality : 0.041 0.145 1365 Planarity : 0.003 0.049 1508 Dihedral : 4.590 49.438 1206 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 2.47 % Allowed : 17.19 % Favored : 80.34 % 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: -0.01 (0.26), residues: 1090 helix: 2.42 (0.28), residues: 365 sheet: -0.97 (0.31), residues: 274 loop : -1.43 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 184 HIS 0.007 0.001 HIS A 205 PHE 0.010 0.001 PHE A 139 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG C 313 ********************** 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 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.408 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: 0.7675 (tmtt) cc_final: 0.7241 (tppt) REVERT: C 276 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 313 ARG cc_start: 0.7205 (ttm-80) cc_final: 0.6596 (ttm-80) REVERT: C 315 ASP cc_start: 0.7738 (t0) cc_final: 0.7454 (p0) REVERT: B 268 ASN cc_start: 0.8614 (m-40) cc_final: 0.7858 (t0) REVERT: B 334 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7657 (m) REVERT: S 91 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 86 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8138 (ttm-80) outliers start: 23 outliers final: 18 residues processed: 160 average time/residue: 0.2837 time to fit residues: 60.8706 Evaluate side-chains 151 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 30 SER Chi-restraints excluded: chain S residue 57 THR 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 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 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN S 82 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 = 0.3774 r_free = 0.3774 target = 0.139022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.093918 restraints weight = 12383.970| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.26 r_work: 0.3027 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8824 Z= 0.158 Angle : 0.569 7.086 11954 Z= 0.294 Chirality : 0.041 0.141 1365 Planarity : 0.003 0.047 1508 Dihedral : 4.533 49.285 1206 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 2.47 % Allowed : 18.05 % Favored : 79.48 % 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: 0.03 (0.26), residues: 1090 helix: 2.44 (0.28), residues: 366 sheet: -0.95 (0.31), residues: 276 loop : -1.41 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.51 seconds wall clock time: 42 minutes 4.43 seconds (2524.43 seconds total)