Starting phenix.real_space_refine on Fri Jun 6 23:54:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc9_37435/06_2025/8wc9_37435_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc9_37435/06_2025/8wc9_37435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wc9_37435/06_2025/8wc9_37435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc9_37435/06_2025/8wc9_37435.map" model { file = "/net/cci-nas-00/data/ceres_data/8wc9_37435/06_2025/8wc9_37435_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc9_37435/06_2025/8wc9_37435_neut.cif" } resolution = 3.2 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 59 5.16 5 C 5350 2.51 5 N 1430 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1801 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2521 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1932 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "S" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1737 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 393 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.63, per 1000 atoms: 0.67 Number of scatterers: 8394 At special positions: 0 Unit cell: (87.55, 122.4, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 59 16.00 O 1554 8.00 N 1430 7.00 C 5350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 1.91 Conformation dependent library (CDL) restraints added in 865.7 milliseconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.4% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.684A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.536A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.547A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.177A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.502A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.666A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.566A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'R' and resid 25 through 28 Processing helix chain 'R' and resid 29 through 49 removed outlier: 3.585A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 86 removed outlier: 3.531A pdb=" N TRP R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Proline residue: R 77 - end of helix removed outlier: 4.087A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 125 removed outlier: 3.595A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 156 removed outlier: 3.585A pdb=" N ILE R 139 " --> pdb=" O ASN R 135 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 177 removed outlier: 3.974A pdb=" N TYR R 171 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 198 removed outlier: 3.754A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 207 Processing helix chain 'R' and resid 207 through 220 removed outlier: 3.776A pdb=" N ARG R 211 " --> pdb=" O PHE R 207 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE R 212 " --> pdb=" O VAL R 208 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 275 removed outlier: 4.365A pdb=" N ILE R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET R 253 " --> pdb=" O THR R 249 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 303 removed outlier: 3.773A pdb=" N ASN R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER R 294 " --> pdb=" O GLY R 290 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.023A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.756A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 35 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.903A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.300A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.861A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.800A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.724A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.339A 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 151 removed outlier: 6.598A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 4.232A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.497A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.509A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.627A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.850A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.663A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1050 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: 2.68 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 1698 1.33 - 1.48: 3286 1.48 - 1.63: 3505 1.63 - 1.79: 14 1.79 - 1.94: 72 Bond restraints: 8575 Sorted by residual: bond pdb=" CA ALA R 302 " pdb=" C ALA R 302 " ideal model delta sigma weight residual 1.525 1.449 0.076 1.11e-02 8.12e+03 4.67e+01 bond pdb=" C ASP R 126 " pdb=" O ASP R 126 " ideal model delta sigma weight residual 1.249 1.204 0.045 8.50e-03 1.38e+04 2.84e+01 bond pdb=" C ALA B 113 " pdb=" O ALA B 113 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" C VAL R 208 " pdb=" O VAL R 208 " ideal model delta sigma weight residual 1.238 1.177 0.060 1.32e-02 5.74e+03 2.09e+01 bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.35e-02 5.49e+03 2.02e+01 ... (remaining 8570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11319 2.41 - 4.82: 279 4.82 - 7.23: 41 7.23 - 9.64: 12 9.64 - 12.05: 2 Bond angle restraints: 11653 Sorted by residual: angle pdb=" N SER B 334 " pdb=" CA SER B 334 " pdb=" C SER B 334 " ideal model delta sigma weight residual 112.58 124.09 -11.51 1.22e+00 6.72e-01 8.91e+01 angle pdb=" N SER R 46 " pdb=" CA SER R 46 " pdb=" C SER R 46 " ideal model delta sigma weight residual 112.89 104.68 8.21 1.24e+00 6.50e-01 4.38e+01 angle pdb=" N ILE R 200 " pdb=" CA ILE R 200 " pdb=" CB ILE R 200 " ideal model delta sigma weight residual 110.50 114.57 -4.07 6.30e-01 2.52e+00 4.18e+01 angle pdb=" C ILE R 32 " pdb=" CA ILE R 32 " pdb=" CB ILE R 32 " ideal model delta sigma weight residual 111.88 104.01 7.87 1.28e+00 6.10e-01 3.78e+01 angle pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" C ASN B 119 " ideal model delta sigma weight residual 111.74 119.77 -8.03 1.35e+00 5.49e-01 3.54e+01 ... (remaining 11648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.16: 4389 14.16 - 28.31: 441 28.31 - 42.46: 157 42.46 - 56.62: 32 56.62 - 70.77: 13 Dihedral angle restraints: 5032 sinusoidal: 1823 harmonic: 3209 Sorted by residual: dihedral pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta harmonic sigma weight residual 122.80 136.44 -13.64 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" C SER B 334 " pdb=" N SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta harmonic sigma weight residual -122.60 -135.71 13.11 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.43 35.57 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 5029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1273 0.121 - 0.241: 47 0.241 - 0.362: 9 0.362 - 0.482: 2 0.482 - 0.603: 1 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" CA PRO R 298 " pdb=" N PRO R 298 " pdb=" C PRO R 298 " pdb=" CB PRO R 298 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA ASN R 40 " pdb=" N ASN R 40 " pdb=" C ASN R 40 " pdb=" CB ASN R 40 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1329 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 200 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO R 201 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO R 201 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 201 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 301 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C TYR R 301 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR R 301 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA R 302 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 193 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C ALA R 193 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA R 193 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE R 194 " 0.015 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1012 2.74 - 3.28: 7891 3.28 - 3.82: 12822 3.82 - 4.36: 15008 4.36 - 4.90: 26922 Nonbonded interactions: 63655 Sorted by model distance: nonbonded pdb=" OG1 THR R 55 " pdb=" OD1 ASN R 58 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.217 3.040 nonbonded pdb=" ND2 ASN B 119 " pdb=" O THR B 143 " model vdw 2.281 3.120 nonbonded pdb=" NH1 ARG S 180 " pdb=" OE1 GLN S 186 " model vdw 2.286 3.120 nonbonded pdb=" NE2 GLN S 3 " pdb=" OG SER S 25 " model vdw 2.289 3.120 ... (remaining 63650 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: 1.080 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.270 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:3.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.076 8578 Z= 0.442 Angle : 0.907 12.047 11659 Z= 0.575 Chirality : 0.064 0.603 1332 Planarity : 0.006 0.104 1480 Dihedral : 13.812 70.775 2949 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.16 % Allowed : 2.43 % Favored : 96.41 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1079 helix: 0.73 (0.28), residues: 369 sheet: -0.03 (0.33), residues: 257 loop : -1.73 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 307 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.002 PHE R 198 TYR 0.023 0.002 TYR R 287 ARG 0.006 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.20900 ( 365) hydrogen bonds : angle 7.37397 ( 1050) SS BOND : bond 0.00371 ( 3) SS BOND : angle 1.65520 ( 6) covalent geometry : bond 0.00735 ( 8575) covalent geometry : angle 0.90661 (11653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7817 (ptmt) cc_final: 0.7296 (pttp) REVERT: A 390 GLU cc_start: 0.7904 (tp30) cc_final: 0.7703 (tp30) REVERT: B 301 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8262 (mtmm) REVERT: R 50 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5807 (t80) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 0.2059 time to fit residues: 43.3116 Evaluate side-chains 133 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN B 239 ASN B 340 ASN R 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.173909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122636 restraints weight = 9937.403| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.63 r_work: 0.3301 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8578 Z= 0.123 Angle : 0.556 6.593 11659 Z= 0.297 Chirality : 0.043 0.170 1332 Planarity : 0.004 0.042 1480 Dihedral : 5.531 64.505 1199 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.27 % Allowed : 9.04 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1079 helix: 1.41 (0.29), residues: 362 sheet: 0.08 (0.33), residues: 272 loop : -1.82 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS A 362 PHE 0.014 0.001 PHE R 303 TYR 0.023 0.001 TYR R 287 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 365) hydrogen bonds : angle 5.07939 ( 1050) SS BOND : bond 0.00405 ( 3) SS BOND : angle 0.75177 ( 6) covalent geometry : bond 0.00260 ( 8575) covalent geometry : angle 0.55630 (11653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7525 (ptmt) cc_final: 0.6911 (pttp) REVERT: B 301 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8060 (mtmm) REVERT: R 50 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.5615 (t80) REVERT: R 119 ASP cc_start: 0.8510 (t0) cc_final: 0.8278 (t0) REVERT: S 18 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7836 (mmm160) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 0.2221 time to fit residues: 41.2467 Evaluate side-chains 127 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 44 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.166767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114101 restraints weight = 10284.787| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.67 r_work: 0.3178 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 8578 Z= 0.293 Angle : 0.702 10.581 11659 Z= 0.374 Chirality : 0.048 0.223 1332 Planarity : 0.005 0.042 1480 Dihedral : 5.917 62.321 1195 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.97 % Allowed : 14.37 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1079 helix: 0.97 (0.28), residues: 368 sheet: 0.02 (0.33), residues: 264 loop : -1.99 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 63 HIS 0.010 0.002 HIS R 62 PHE 0.016 0.002 PHE B 151 TYR 0.020 0.002 TYR S 190 ARG 0.006 0.001 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.06689 ( 365) hydrogen bonds : angle 5.18741 ( 1050) SS BOND : bond 0.00572 ( 3) SS BOND : angle 1.39867 ( 6) covalent geometry : bond 0.00720 ( 8575) covalent geometry : angle 0.70104 (11653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.864 Fit side-chains REVERT: A 274 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7141 (pttp) REVERT: B 59 TYR cc_start: 0.8436 (m-80) cc_final: 0.7413 (m-80) REVERT: B 301 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8144 (mtmm) REVERT: R 50 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.5598 (t80) outliers start: 17 outliers final: 13 residues processed: 137 average time/residue: 0.2032 time to fit residues: 38.3249 Evaluate side-chains 136 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 44 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.170098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118451 restraints weight = 9967.320| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.62 r_work: 0.3238 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8578 Z= 0.140 Angle : 0.554 6.306 11659 Z= 0.297 Chirality : 0.043 0.218 1332 Planarity : 0.004 0.043 1480 Dihedral : 5.296 63.362 1194 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.20 % Allowed : 16.11 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1079 helix: 1.30 (0.29), residues: 365 sheet: 0.02 (0.33), residues: 270 loop : -1.88 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.006 0.001 HIS A 362 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR S 190 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 365) hydrogen bonds : angle 4.81704 ( 1050) SS BOND : bond 0.00452 ( 3) SS BOND : angle 0.90574 ( 6) covalent geometry : bond 0.00323 ( 8575) covalent geometry : angle 0.55387 (11653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.848 Fit side-chains REVERT: A 274 LYS cc_start: 0.7714 (ptmt) cc_final: 0.7083 (pttp) REVERT: B 59 TYR cc_start: 0.8314 (m-80) cc_final: 0.7575 (m-80) REVERT: B 273 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 301 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7748 (mtmm) REVERT: B 303 ASP cc_start: 0.7585 (m-30) cc_final: 0.7223 (m-30) REVERT: R 50 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.5680 (t80) REVERT: R 119 ASP cc_start: 0.8551 (t0) cc_final: 0.8305 (t0) outliers start: 19 outliers final: 10 residues processed: 141 average time/residue: 0.2206 time to fit residues: 41.7853 Evaluate side-chains 135 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.0470 chunk 6 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 44 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131356 restraints weight = 10016.544| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.89 r_work: 0.3263 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8578 Z= 0.101 Angle : 0.508 5.710 11659 Z= 0.272 Chirality : 0.042 0.219 1332 Planarity : 0.004 0.041 1480 Dihedral : 4.533 51.138 1192 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 17.38 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1079 helix: 1.58 (0.29), residues: 364 sheet: 0.05 (0.32), residues: 275 loop : -1.67 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.005 0.001 HIS A 362 PHE 0.010 0.001 PHE B 199 TYR 0.021 0.001 TYR R 287 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 365) hydrogen bonds : angle 4.57287 ( 1050) SS BOND : bond 0.00398 ( 3) SS BOND : angle 0.74615 ( 6) covalent geometry : bond 0.00211 ( 8575) covalent geometry : angle 0.50761 (11653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.966 Fit side-chains REVERT: A 274 LYS cc_start: 0.7659 (ptmt) cc_final: 0.7052 (pttp) REVERT: A 280 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7479 (ttp-110) REVERT: B 59 TYR cc_start: 0.8264 (m-80) cc_final: 0.7713 (m-80) REVERT: B 75 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: B 264 TYR cc_start: 0.8518 (m-80) cc_final: 0.8303 (m-80) REVERT: B 303 ASP cc_start: 0.7525 (m-30) cc_final: 0.7163 (m-30) REVERT: R 50 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.5528 (t80) REVERT: R 119 ASP cc_start: 0.8470 (t70) cc_final: 0.8234 (t0) outliers start: 17 outliers final: 6 residues processed: 140 average time/residue: 0.2220 time to fit residues: 42.1784 Evaluate side-chains 132 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 259 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116862 restraints weight = 9890.237| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.63 r_work: 0.3225 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8578 Z= 0.162 Angle : 0.563 7.368 11659 Z= 0.301 Chirality : 0.044 0.224 1332 Planarity : 0.004 0.040 1480 Dihedral : 4.744 51.594 1192 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.97 % Allowed : 17.27 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1079 helix: 1.49 (0.28), residues: 365 sheet: 0.19 (0.33), residues: 263 loop : -1.80 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.005 0.001 HIS A 362 PHE 0.012 0.001 PHE A 376 TYR 0.018 0.002 TYR R 287 ARG 0.003 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 365) hydrogen bonds : angle 4.67430 ( 1050) SS BOND : bond 0.00481 ( 3) SS BOND : angle 0.98548 ( 6) covalent geometry : bond 0.00382 ( 8575) covalent geometry : angle 0.56261 (11653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.861 Fit side-chains REVERT: A 274 LYS cc_start: 0.7797 (ptmt) cc_final: 0.7172 (pttp) REVERT: A 280 ARG cc_start: 0.7833 (ttp-110) cc_final: 0.7566 (ttp-110) REVERT: A 307 LYS cc_start: 0.5777 (mmtt) cc_final: 0.5455 (mmtm) REVERT: B 75 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: B 273 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8360 (mp) REVERT: R 50 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.5468 (t80) REVERT: R 119 ASP cc_start: 0.8557 (t70) cc_final: 0.8279 (t0) outliers start: 17 outliers final: 11 residues processed: 133 average time/residue: 0.2142 time to fit residues: 38.4389 Evaluate side-chains 133 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 259 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120240 restraints weight = 10155.160| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.76 r_work: 0.3267 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8578 Z= 0.108 Angle : 0.513 7.027 11659 Z= 0.274 Chirality : 0.042 0.208 1332 Planarity : 0.003 0.040 1480 Dihedral : 4.471 50.957 1192 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.74 % Allowed : 17.73 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1079 helix: 1.73 (0.29), residues: 360 sheet: 0.12 (0.32), residues: 275 loop : -1.63 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 362 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR S 190 ARG 0.003 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 365) hydrogen bonds : angle 4.50567 ( 1050) SS BOND : bond 0.00418 ( 3) SS BOND : angle 0.77874 ( 6) covalent geometry : bond 0.00239 ( 8575) covalent geometry : angle 0.51265 (11653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.961 Fit side-chains REVERT: A 274 LYS cc_start: 0.7783 (ptmt) cc_final: 0.7181 (pttp) REVERT: A 280 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.7516 (ttp-110) REVERT: A 307 LYS cc_start: 0.5772 (mmtt) cc_final: 0.5460 (mmtm) REVERT: B 59 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: B 75 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: R 50 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.5357 (t80) REVERT: R 119 ASP cc_start: 0.8520 (t70) cc_final: 0.8263 (t0) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 0.2298 time to fit residues: 40.5177 Evaluate side-chains 136 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 259 GLN R 297 ASN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116605 restraints weight = 10188.856| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.67 r_work: 0.3193 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8578 Z= 0.224 Angle : 0.620 8.956 11659 Z= 0.332 Chirality : 0.046 0.195 1332 Planarity : 0.004 0.039 1480 Dihedral : 5.017 51.433 1192 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.78 % Allowed : 17.15 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1079 helix: 1.31 (0.28), residues: 371 sheet: 0.11 (0.33), residues: 270 loop : -1.83 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.006 0.002 HIS A 362 PHE 0.014 0.002 PHE B 151 TYR 0.020 0.002 TYR S 190 ARG 0.003 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.05758 ( 365) hydrogen bonds : angle 4.81230 ( 1050) SS BOND : bond 0.00532 ( 3) SS BOND : angle 1.17829 ( 6) covalent geometry : bond 0.00548 ( 8575) covalent geometry : angle 0.61959 (11653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.881 Fit side-chains REVERT: A 274 LYS cc_start: 0.7822 (ptmt) cc_final: 0.7200 (pttp) REVERT: A 280 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7574 (ttp-110) REVERT: A 307 LYS cc_start: 0.6055 (mmtt) cc_final: 0.5805 (mmtt) REVERT: B 75 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: B 273 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8415 (mp) REVERT: R 50 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.5352 (t80) REVERT: R 119 ASP cc_start: 0.8548 (t70) cc_final: 0.8275 (t0) REVERT: R 219 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.5754 (mp10) outliers start: 24 outliers final: 17 residues processed: 140 average time/residue: 0.2364 time to fit residues: 45.0932 Evaluate side-chains 142 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120079 restraints weight = 10004.451| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.67 r_work: 0.3271 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8578 Z= 0.106 Angle : 0.516 6.658 11659 Z= 0.276 Chirality : 0.042 0.217 1332 Planarity : 0.003 0.039 1480 Dihedral : 4.511 51.102 1192 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.32 % Allowed : 18.31 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1079 helix: 1.74 (0.29), residues: 359 sheet: 0.21 (0.33), residues: 269 loop : -1.69 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 362 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR S 59 ARG 0.003 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 365) hydrogen bonds : angle 4.51842 ( 1050) SS BOND : bond 0.00382 ( 3) SS BOND : angle 0.73743 ( 6) covalent geometry : bond 0.00227 ( 8575) covalent geometry : angle 0.51556 (11653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.320 Fit side-chains REVERT: A 274 LYS cc_start: 0.7791 (ptmt) cc_final: 0.7181 (pttp) REVERT: A 280 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7481 (ttp-110) REVERT: B 75 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: R 50 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.5368 (t80) REVERT: R 119 ASP cc_start: 0.8518 (t70) cc_final: 0.8258 (t0) REVERT: S 18 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7619 (mmm-85) outliers start: 20 outliers final: 16 residues processed: 135 average time/residue: 0.2771 time to fit residues: 50.9214 Evaluate side-chains 136 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.0070 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.172452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120542 restraints weight = 9939.775| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.65 r_work: 0.3275 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8578 Z= 0.107 Angle : 0.511 6.776 11659 Z= 0.273 Chirality : 0.042 0.224 1332 Planarity : 0.003 0.040 1480 Dihedral : 4.377 50.828 1192 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.09 % Allowed : 18.19 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1079 helix: 1.80 (0.29), residues: 359 sheet: 0.19 (0.33), residues: 272 loop : -1.61 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS A 362 PHE 0.010 0.001 PHE B 199 TYR 0.020 0.001 TYR R 287 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 365) hydrogen bonds : angle 4.40688 ( 1050) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.73844 ( 6) covalent geometry : bond 0.00234 ( 8575) covalent geometry : angle 0.51039 (11653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.959 Fit side-chains REVERT: A 274 LYS cc_start: 0.7791 (ptmt) cc_final: 0.7193 (pttp) REVERT: B 59 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: B 75 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: R 50 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6076 (t80) REVERT: R 119 ASP cc_start: 0.8422 (t70) cc_final: 0.8185 (t0) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.2474 time to fit residues: 44.6614 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.6980 chunk 93 optimal weight: 0.0470 chunk 8 optimal weight: 0.0270 chunk 34 optimal weight: 0.0050 chunk 57 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125277 restraints weight = 10050.604| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.69 r_work: 0.3328 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8578 Z= 0.095 Angle : 0.496 6.625 11659 Z= 0.262 Chirality : 0.041 0.217 1332 Planarity : 0.003 0.040 1480 Dihedral : 4.128 50.443 1192 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.51 % Allowed : 19.12 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1079 helix: 2.05 (0.29), residues: 352 sheet: 0.14 (0.32), residues: 279 loop : -1.52 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 59 HIS 0.004 0.001 HIS A 362 PHE 0.009 0.001 PHE A 376 TYR 0.024 0.001 TYR R 287 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 365) hydrogen bonds : angle 4.25505 ( 1050) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.63319 ( 6) covalent geometry : bond 0.00195 ( 8575) covalent geometry : angle 0.49610 (11653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.41 seconds wall clock time: 89 minutes 28.58 seconds (5368.58 seconds total)