Starting phenix.real_space_refine on Tue Apr 29 09:16:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z68_39795/04_2025/8z68_39795_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z68_39795/04_2025/8z68_39795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z68_39795/04_2025/8z68_39795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z68_39795/04_2025/8z68_39795.map" model { file = "/net/cci-nas-00/data/ceres_data/8z68_39795/04_2025/8z68_39795_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z68_39795/04_2025/8z68_39795_neut.cif" } resolution = 2.64 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= 0.001 sd= 0.022 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 50 5.16 5 C 5468 2.51 5 N 1470 2.21 5 O 1555 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-5669/modules/chem_data/mon_lib" Total number of atoms: 8543 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1845 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2456 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 338 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "S" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1730 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2174 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 276} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 5.61, per 1000 atoms: 0.66 Number of scatterers: 8543 At special positions: 0 Unit cell: (86.48, 118.68, 127.88, 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 50 16.00 O 1555 8.00 N 1470 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 13 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 172 " 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.5% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.545A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.617A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.946A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.386A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.531A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.270A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.643A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing helix chain 'R' and resid 18 through 23 Processing helix chain 'R' and resid 23 through 36 Processing helix chain 'R' and resid 37 through 52 removed outlier: 4.755A pdb=" N LEU R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 83 removed outlier: 3.926A pdb=" N TYR R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 89 through 103 removed outlier: 4.209A pdb=" N SER R 93 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 125 Processing helix chain 'R' and resid 134 through 159 removed outlier: 4.384A pdb=" N TYR R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS R 159 " --> pdb=" O TYR R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 192 Processing helix chain 'R' and resid 194 through 205 Processing helix chain 'R' and resid 207 through 212 Processing helix chain 'R' and resid 219 through 254 removed outlier: 3.650A pdb=" N GLN R 227 " --> pdb=" O LYS R 223 " (cutoff:3.500A) Proline residue: R 243 - end of helix removed outlier: 3.657A pdb=" N TRP R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 276 removed outlier: 3.540A pdb=" N ALA R 261 " --> pdb=" O SER R 257 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA R 267 " --> pdb=" O GLY R 263 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 296 removed outlier: 3.539A pdb=" N HIS R 294 " --> pdb=" O SER R 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG R 295 " --> pdb=" O GLU R 291 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP R 296 " --> pdb=" O THR R 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 290 through 296' Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.552A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.780A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.562A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.328A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.574A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.901A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.629A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.817A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.902A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.616A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 162 through 164 450 hydrogen bonds defined for protein. 1272 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: 2.62 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1356 1.28 - 1.41: 2382 1.41 - 1.55: 4935 1.55 - 1.68: 0 1.68 - 1.81: 67 Bond restraints: 8740 Sorted by residual: bond pdb=" C ILE R 154 " pdb=" O ILE R 154 " ideal model delta sigma weight residual 1.237 1.155 0.081 1.12e-02 7.97e+03 5.26e+01 bond pdb=" C ASP R 67 " pdb=" O ASP R 67 " ideal model delta sigma weight residual 1.237 1.151 0.085 1.19e-02 7.06e+03 5.16e+01 bond pdb=" CA LYS R 223 " pdb=" C LYS R 223 " ideal model delta sigma weight residual 1.523 1.428 0.095 1.35e-02 5.49e+03 4.93e+01 bond pdb=" C THR R 30 " pdb=" O THR R 30 " ideal model delta sigma weight residual 1.237 1.160 0.076 1.19e-02 7.06e+03 4.13e+01 bond pdb=" C VAL R 31 " pdb=" O VAL R 31 " ideal model delta sigma weight residual 1.237 1.155 0.082 1.29e-02 6.01e+03 4.03e+01 ... (remaining 8735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 11777 3.05 - 6.11: 114 6.11 - 9.16: 16 9.16 - 12.21: 8 12.21 - 15.27: 2 Bond angle restraints: 11917 Sorted by residual: angle pdb=" N THR R 152 " pdb=" CA THR R 152 " pdb=" C THR R 152 " ideal model delta sigma weight residual 113.55 101.27 12.28 1.26e+00 6.30e-01 9.50e+01 angle pdb=" C VAL R 26 " pdb=" CA VAL R 26 " pdb=" CB VAL R 26 " ideal model delta sigma weight residual 111.97 102.21 9.76 1.28e+00 6.10e-01 5.82e+01 angle pdb=" C ILE R 154 " pdb=" CA ILE R 154 " pdb=" CB ILE R 154 " ideal model delta sigma weight residual 112.02 102.38 9.64 1.31e+00 5.83e-01 5.41e+01 angle pdb=" N ALA R 147 " pdb=" CA ALA R 147 " pdb=" C ALA R 147 " ideal model delta sigma weight residual 111.07 103.73 7.34 1.07e+00 8.73e-01 4.70e+01 angle pdb=" CA TYR R 176 " pdb=" CB TYR R 176 " pdb=" CG TYR R 176 " ideal model delta sigma weight residual 113.90 102.29 11.61 1.80e+00 3.09e-01 4.16e+01 ... (remaining 11912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4605 17.95 - 35.90: 386 35.90 - 53.85: 73 53.85 - 71.80: 12 71.80 - 89.75: 5 Dihedral angle restraints: 5081 sinusoidal: 1758 harmonic: 3323 Sorted by residual: dihedral pdb=" N ARG R 213 " pdb=" C ARG R 213 " pdb=" CA ARG R 213 " pdb=" CB ARG R 213 " ideal model delta harmonic sigma weight residual 122.80 136.41 -13.61 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" N HIS R 175 " pdb=" C HIS R 175 " pdb=" CA HIS R 175 " pdb=" CB HIS R 175 " ideal model delta harmonic sigma weight residual 122.80 110.16 12.64 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" N VAL R 253 " pdb=" C VAL R 253 " pdb=" CA VAL R 253 " pdb=" CB VAL R 253 " ideal model delta harmonic sigma weight residual 123.40 135.30 -11.90 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 5078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1335 0.112 - 0.224: 34 0.224 - 0.336: 10 0.336 - 0.448: 0 0.448 - 0.560: 4 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA VAL R 253 " pdb=" N VAL R 253 " pdb=" C VAL R 253 " pdb=" CB VAL R 253 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA ARG R 213 " pdb=" N ARG R 213 " pdb=" C ARG R 213 " pdb=" CB ARG R 213 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CA THR R 30 " pdb=" N THR R 30 " pdb=" C THR R 30 " pdb=" CB THR R 30 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.07e+00 ... (remaining 1380 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 248 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C LEU R 248 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU R 248 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU R 249 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 223 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LYS R 223 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS R 223 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP R 224 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 176 " 0.034 2.00e-02 2.50e+03 2.22e-02 9.85e+00 pdb=" CG TYR R 176 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 176 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 176 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 176 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 176 " 0.007 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 263 2.69 - 3.24: 8316 3.24 - 3.80: 14088 3.80 - 4.35: 18444 4.35 - 4.90: 31056 Nonbonded interactions: 72167 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.138 3.040 nonbonded pdb=" O LEU R 272 " pdb=" OG1 THR R 275 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR R 102 " pdb=" OE1 GLU R 174 " model vdw 2.207 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O GLU B 130 " model vdw 2.235 3.040 ... (remaining 72162 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: 1.880 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: 0.090 Process input model: 23.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.009 0.095 8743 Z= 0.543 Angle : 0.797 15.268 11923 Z= 0.478 Chirality : 0.058 0.560 1383 Planarity : 0.005 0.072 1511 Dihedral : 14.044 89.752 2928 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.82 % Allowed : 6.69 % Favored : 92.49 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.03 % 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: 0.19 (0.25), residues: 1122 helix: 1.15 (0.28), residues: 378 sheet: 0.02 (0.29), residues: 284 loop : -0.57 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.008 0.001 HIS B 183 PHE 0.027 0.002 PHE R 173 TYR 0.052 0.002 TYR R 176 ARG 0.007 0.001 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.13675 ( 445) hydrogen bonds : angle 6.38731 ( 1272) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.66988 ( 6) covalent geometry : bond 0.00863 ( 8740) covalent geometry : angle 0.79747 (11917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 0.891 Fit side-chains REVERT: A 243 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7903 (mptp) REVERT: A 265 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8290 (mtp-110) REVERT: A 310 ASP cc_start: 0.8253 (m-30) cc_final: 0.8019 (m-30) REVERT: A 331 ASP cc_start: 0.7718 (m-30) cc_final: 0.7492 (m-30) REVERT: B 219 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: B 269 ILE cc_start: 0.8226 (pt) cc_final: 0.7784 (pp) REVERT: G 38 MET cc_start: 0.7703 (mtm) cc_final: 0.7447 (ttm) REVERT: S 68 PHE cc_start: 0.7756 (m-10) cc_final: 0.7542 (m-10) REVERT: S 85 SER cc_start: 0.8538 (t) cc_final: 0.8334 (t) REVERT: S 181 SER cc_start: 0.8316 (t) cc_final: 0.8060 (p) REVERT: S 218 MET cc_start: 0.8576 (ttp) cc_final: 0.8206 (ttm) REVERT: R 81 VAL cc_start: 0.7966 (m) cc_final: 0.7738 (p) REVERT: R 106 TYR cc_start: 0.8226 (m-80) cc_final: 0.7803 (m-80) REVERT: R 132 PHE cc_start: 0.7873 (m-80) cc_final: 0.7455 (m-80) REVERT: R 179 GLN cc_start: 0.7058 (mm110) cc_final: 0.6858 (mt0) REVERT: R 200 LEU cc_start: 0.7432 (tp) cc_final: 0.7228 (tt) outliers start: 7 outliers final: 3 residues processed: 215 average time/residue: 1.1074 time to fit residues: 258.3557 Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 161 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN A 390 GLN B 62 HIS B 88 ASN B 119 ASN B 125 ASN B 293 ASN R 54 ASN R 125 HIS R 167 ASN R 269 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108481 restraints weight = 12374.030| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.51 r_work: 0.3427 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8743 Z= 0.186 Angle : 0.568 6.100 11923 Z= 0.307 Chirality : 0.043 0.200 1383 Planarity : 0.004 0.043 1511 Dihedral : 5.077 49.730 1236 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.70 % Allowed : 12.09 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.37 (0.25), residues: 1122 helix: 1.46 (0.28), residues: 382 sheet: 0.02 (0.29), residues: 289 loop : -0.56 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.014 0.002 PHE B 253 TYR 0.033 0.002 TYR B 59 ARG 0.005 0.001 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 445) hydrogen bonds : angle 5.08010 ( 1272) SS BOND : bond 0.00534 ( 3) SS BOND : angle 1.13623 ( 6) covalent geometry : bond 0.00424 ( 8740) covalent geometry : angle 0.56748 (11917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 331 ASP cc_start: 0.7594 (m-30) cc_final: 0.7370 (m-30) REVERT: B 237 ASN cc_start: 0.7292 (t0) cc_final: 0.6942 (t0) REVERT: B 269 ILE cc_start: 0.8293 (pt) cc_final: 0.7902 (pp) REVERT: G 38 MET cc_start: 0.7775 (mtm) cc_final: 0.7514 (ttp) REVERT: S 85 SER cc_start: 0.8558 (t) cc_final: 0.8182 (p) REVERT: S 128 MET cc_start: 0.8773 (mmp) cc_final: 0.8565 (tpp) REVERT: S 192 SER cc_start: 0.8684 (t) cc_final: 0.8365 (p) REVERT: S 218 MET cc_start: 0.8574 (ttp) cc_final: 0.8251 (ttm) REVERT: R 106 TYR cc_start: 0.8396 (m-80) cc_final: 0.8153 (m-80) REVERT: R 132 PHE cc_start: 0.8186 (m-80) cc_final: 0.7772 (m-80) REVERT: R 156 PHE cc_start: 0.7737 (m-80) cc_final: 0.7358 (m-80) REVERT: R 247 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7792 (tt) outliers start: 23 outliers final: 10 residues processed: 230 average time/residue: 1.1779 time to fit residues: 291.9880 Evaluate side-chains 219 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 212 VAL Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 292 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN B 88 ASN B 125 ASN B 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107589 restraints weight = 12659.292| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.52 r_work: 0.3425 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8743 Z= 0.172 Angle : 0.542 5.545 11923 Z= 0.294 Chirality : 0.042 0.174 1383 Planarity : 0.004 0.044 1511 Dihedral : 4.922 48.161 1233 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.93 % Allowed : 15.49 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.50 (0.26), residues: 1122 helix: 1.61 (0.28), residues: 385 sheet: 0.08 (0.30), residues: 283 loop : -0.55 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.014 0.002 PHE B 151 TYR 0.028 0.002 TYR B 59 ARG 0.009 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 445) hydrogen bonds : angle 4.95256 ( 1272) SS BOND : bond 0.00370 ( 3) SS BOND : angle 0.82166 ( 6) covalent geometry : bond 0.00389 ( 8740) covalent geometry : angle 0.54177 (11917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 1.008 Fit side-chains REVERT: A 331 ASP cc_start: 0.7651 (m-30) cc_final: 0.7421 (m-30) REVERT: B 269 ILE cc_start: 0.8294 (pt) cc_final: 0.7892 (pp) REVERT: G 38 MET cc_start: 0.7772 (mtm) cc_final: 0.7503 (ttp) REVERT: S 85 SER cc_start: 0.8571 (t) cc_final: 0.8203 (p) REVERT: S 128 MET cc_start: 0.8768 (mmp) cc_final: 0.8563 (tpp) REVERT: S 218 MET cc_start: 0.8583 (ttp) cc_final: 0.8264 (ttm) REVERT: R 132 PHE cc_start: 0.8193 (m-80) cc_final: 0.7789 (m-80) REVERT: R 173 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7430 (t80) outliers start: 25 outliers final: 10 residues processed: 225 average time/residue: 1.0707 time to fit residues: 260.2848 Evaluate side-chains 225 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 0.0060 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN B 119 ASN B 125 ASN B 293 ASN S 130 GLN R 104 ASN R 159 HIS R 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107118 restraints weight = 12523.931| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.53 r_work: 0.3413 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8743 Z= 0.174 Angle : 0.544 5.717 11923 Z= 0.295 Chirality : 0.042 0.170 1383 Planarity : 0.004 0.044 1511 Dihedral : 4.893 45.985 1233 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.93 % Allowed : 18.19 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.51 (0.26), residues: 1122 helix: 1.60 (0.28), residues: 385 sheet: 0.15 (0.29), residues: 290 loop : -0.58 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.015 0.002 PHE B 253 TYR 0.027 0.002 TYR B 59 ARG 0.008 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 445) hydrogen bonds : angle 4.88747 ( 1272) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.83867 ( 6) covalent geometry : bond 0.00398 ( 8740) covalent geometry : angle 0.54373 (11917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.862 Fit side-chains REVERT: A 331 ASP cc_start: 0.7675 (m-30) cc_final: 0.7467 (m-30) REVERT: B 49 ARG cc_start: 0.8516 (mmt90) cc_final: 0.8294 (mmt-90) REVERT: B 96 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7853 (mtt180) REVERT: B 188 MET cc_start: 0.8459 (mmm) cc_final: 0.8181 (mmp) REVERT: B 269 ILE cc_start: 0.8319 (pt) cc_final: 0.7935 (pp) REVERT: G 38 MET cc_start: 0.7764 (mtm) cc_final: 0.7495 (ttp) REVERT: S 69 THR cc_start: 0.8058 (t) cc_final: 0.7839 (m) REVERT: S 85 SER cc_start: 0.8565 (t) cc_final: 0.8196 (p) REVERT: S 128 MET cc_start: 0.8743 (mmp) cc_final: 0.8523 (tpp) REVERT: S 218 MET cc_start: 0.8579 (ttp) cc_final: 0.8242 (ttm) REVERT: R 106 TYR cc_start: 0.8526 (m-80) cc_final: 0.8074 (m-80) REVERT: R 132 PHE cc_start: 0.8204 (m-80) cc_final: 0.7799 (m-80) REVERT: R 173 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7513 (t80) outliers start: 25 outliers final: 12 residues processed: 223 average time/residue: 0.9219 time to fit residues: 222.2803 Evaluate side-chains 223 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.5980 chunk 87 optimal weight: 0.0970 chunk 7 optimal weight: 0.4980 chunk 110 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN B 125 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.119491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108867 restraints weight = 12381.600| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.52 r_work: 0.3432 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8743 Z= 0.126 Angle : 0.523 7.860 11923 Z= 0.282 Chirality : 0.041 0.150 1383 Planarity : 0.003 0.045 1511 Dihedral : 4.772 46.255 1233 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.70 % Allowed : 18.78 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1122 helix: 1.65 (0.28), residues: 387 sheet: 0.08 (0.29), residues: 293 loop : -0.57 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.006 0.001 HIS R 269 PHE 0.015 0.001 PHE B 253 TYR 0.018 0.001 TYR B 59 ARG 0.007 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 445) hydrogen bonds : angle 4.76092 ( 1272) SS BOND : bond 0.00209 ( 3) SS BOND : angle 0.66229 ( 6) covalent geometry : bond 0.00283 ( 8740) covalent geometry : angle 0.52337 (11917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.887 Fit side-chains REVERT: A 331 ASP cc_start: 0.7630 (m-30) cc_final: 0.7416 (m-30) REVERT: B 49 ARG cc_start: 0.8491 (mmt90) cc_final: 0.8247 (mmt-90) REVERT: B 96 ARG cc_start: 0.8137 (ptp-170) cc_final: 0.7824 (mtt180) REVERT: B 188 MET cc_start: 0.8484 (mmm) cc_final: 0.8207 (mmp) REVERT: B 269 ILE cc_start: 0.8306 (pt) cc_final: 0.7916 (pp) REVERT: G 38 MET cc_start: 0.7711 (mtm) cc_final: 0.7434 (ttp) REVERT: S 69 THR cc_start: 0.8019 (t) cc_final: 0.7809 (m) REVERT: S 85 SER cc_start: 0.8552 (t) cc_final: 0.8198 (p) REVERT: S 128 MET cc_start: 0.8750 (mmp) cc_final: 0.8515 (tpp) REVERT: S 218 MET cc_start: 0.8584 (ttp) cc_final: 0.8271 (ttm) REVERT: R 106 TYR cc_start: 0.8543 (m-80) cc_final: 0.8089 (m-80) REVERT: R 132 PHE cc_start: 0.8152 (m-80) cc_final: 0.7749 (m-80) REVERT: R 173 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7490 (t80) outliers start: 23 outliers final: 12 residues processed: 225 average time/residue: 0.9012 time to fit residues: 219.5944 Evaluate side-chains 226 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 125 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.118154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107488 restraints weight = 12567.548| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.54 r_work: 0.3424 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8743 Z= 0.159 Angle : 0.537 6.540 11923 Z= 0.289 Chirality : 0.042 0.163 1383 Planarity : 0.004 0.045 1511 Dihedral : 4.799 43.824 1233 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.46 % Allowed : 20.66 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.48 (0.26), residues: 1122 helix: 1.57 (0.28), residues: 389 sheet: 0.08 (0.30), residues: 288 loop : -0.56 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE R 265 TYR 0.019 0.002 TYR R 70 ARG 0.008 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 445) hydrogen bonds : angle 4.75031 ( 1272) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.74473 ( 6) covalent geometry : bond 0.00364 ( 8740) covalent geometry : angle 0.53682 (11917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.954 Fit side-chains REVERT: A 59 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7783 (mm-40) REVERT: A 331 ASP cc_start: 0.7668 (m-30) cc_final: 0.7456 (m-30) REVERT: B 96 ARG cc_start: 0.8171 (ptp-170) cc_final: 0.7866 (mtt180) REVERT: B 155 ASN cc_start: 0.8330 (t0) cc_final: 0.8053 (t0) REVERT: B 188 MET cc_start: 0.8460 (mmm) cc_final: 0.8190 (mmp) REVERT: B 269 ILE cc_start: 0.8316 (pt) cc_final: 0.7930 (pp) REVERT: G 38 MET cc_start: 0.7705 (mtm) cc_final: 0.7432 (ttp) REVERT: S 69 THR cc_start: 0.8034 (t) cc_final: 0.7834 (m) REVERT: S 85 SER cc_start: 0.8572 (t) cc_final: 0.8216 (p) REVERT: S 128 MET cc_start: 0.8765 (mmp) cc_final: 0.8528 (tpp) REVERT: S 218 MET cc_start: 0.8628 (ttp) cc_final: 0.8308 (ttm) REVERT: R 106 TYR cc_start: 0.8532 (m-80) cc_final: 0.8060 (m-80) REVERT: R 132 PHE cc_start: 0.8194 (m-80) cc_final: 0.7862 (m-80) REVERT: R 170 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7999 (ptm160) REVERT: R 244 TYR cc_start: 0.8368 (t80) cc_final: 0.8147 (t80) REVERT: R 260 PHE cc_start: 0.7297 (t80) cc_final: 0.7047 (t80) outliers start: 21 outliers final: 11 residues processed: 214 average time/residue: 0.9746 time to fit residues: 224.9006 Evaluate side-chains 222 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106897 restraints weight = 12577.589| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.53 r_work: 0.3414 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8743 Z= 0.186 Angle : 0.560 7.087 11923 Z= 0.302 Chirality : 0.043 0.170 1383 Planarity : 0.004 0.045 1511 Dihedral : 4.813 35.893 1233 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 20.31 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.45 (0.26), residues: 1122 helix: 1.55 (0.28), residues: 387 sheet: 0.10 (0.30), residues: 284 loop : -0.61 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.006 0.001 HIS R 269 PHE 0.017 0.002 PHE R 265 TYR 0.026 0.002 TYR R 268 ARG 0.009 0.001 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 445) hydrogen bonds : angle 4.79975 ( 1272) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.86389 ( 6) covalent geometry : bond 0.00424 ( 8740) covalent geometry : angle 0.55971 (11917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.912 Fit side-chains REVERT: A 59 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7828 (mm-40) REVERT: A 331 ASP cc_start: 0.7687 (m-30) cc_final: 0.7480 (m-30) REVERT: B 59 TYR cc_start: 0.8090 (m-80) cc_final: 0.7719 (m-80) REVERT: B 96 ARG cc_start: 0.8207 (ptp-170) cc_final: 0.7864 (mtt180) REVERT: B 155 ASN cc_start: 0.8371 (t0) cc_final: 0.8011 (t0) REVERT: B 269 ILE cc_start: 0.8288 (pt) cc_final: 0.7897 (pp) REVERT: G 38 MET cc_start: 0.7743 (mtm) cc_final: 0.7477 (ttp) REVERT: S 85 SER cc_start: 0.8586 (t) cc_final: 0.8230 (p) REVERT: S 128 MET cc_start: 0.8774 (mmp) cc_final: 0.8482 (tpp) REVERT: S 218 MET cc_start: 0.8625 (ttp) cc_final: 0.8277 (ttm) REVERT: R 106 TYR cc_start: 0.8566 (m-80) cc_final: 0.8078 (m-80) REVERT: R 132 PHE cc_start: 0.8209 (m-80) cc_final: 0.7819 (m-80) outliers start: 27 outliers final: 15 residues processed: 215 average time/residue: 0.9601 time to fit residues: 223.9144 Evaluate side-chains 215 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN ** R 269 HIS ** 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 = 0.3663 r_free = 0.3663 target = 0.119023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108470 restraints weight = 12712.117| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.54 r_work: 0.3439 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8743 Z= 0.132 Angle : 0.538 8.085 11923 Z= 0.289 Chirality : 0.041 0.146 1383 Planarity : 0.004 0.046 1511 Dihedral : 4.659 31.949 1233 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.82 % Allowed : 20.89 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.49 (0.26), residues: 1122 helix: 1.64 (0.28), residues: 386 sheet: 0.12 (0.30), residues: 288 loop : -0.63 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 265 TYR 0.023 0.001 TYR R 268 ARG 0.009 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 445) hydrogen bonds : angle 4.67491 ( 1272) SS BOND : bond 0.00107 ( 3) SS BOND : angle 1.31216 ( 6) covalent geometry : bond 0.00297 ( 8740) covalent geometry : angle 0.53711 (11917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.909 Fit side-chains REVERT: A 29 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8031 (tp-100) REVERT: A 59 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7758 (mm-40) REVERT: A 331 ASP cc_start: 0.7622 (m-30) cc_final: 0.7411 (m-30) REVERT: A 347 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7967 (ttp80) REVERT: B 96 ARG cc_start: 0.8127 (ptp-170) cc_final: 0.7801 (mtt180) REVERT: B 155 ASN cc_start: 0.8345 (t0) cc_final: 0.8027 (t0) REVERT: B 269 ILE cc_start: 0.8329 (pt) cc_final: 0.7944 (pp) REVERT: G 38 MET cc_start: 0.7672 (mtm) cc_final: 0.7396 (ttp) REVERT: S 85 SER cc_start: 0.8594 (t) cc_final: 0.8239 (p) REVERT: S 128 MET cc_start: 0.8725 (mmp) cc_final: 0.8448 (tpp) REVERT: S 218 MET cc_start: 0.8542 (ttp) cc_final: 0.8213 (ttm) REVERT: R 106 TYR cc_start: 0.8545 (m-80) cc_final: 0.8030 (m-80) REVERT: R 132 PHE cc_start: 0.8175 (m-80) cc_final: 0.7794 (m-80) REVERT: R 244 TYR cc_start: 0.8343 (t80) cc_final: 0.8058 (t80) REVERT: R 249 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7538 (tp) outliers start: 24 outliers final: 13 residues processed: 211 average time/residue: 1.1218 time to fit residues: 256.4396 Evaluate side-chains 213 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 101 optimal weight: 0.0970 chunk 106 optimal weight: 0.2980 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.119125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108587 restraints weight = 12706.863| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.54 r_work: 0.3442 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8743 Z= 0.135 Angle : 0.548 8.511 11923 Z= 0.292 Chirality : 0.041 0.149 1383 Planarity : 0.004 0.045 1511 Dihedral : 4.622 28.138 1233 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 21.95 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1122 helix: 1.68 (0.28), residues: 386 sheet: 0.09 (0.29), residues: 293 loop : -0.60 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 265 TYR 0.022 0.001 TYR R 268 ARG 0.008 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 445) hydrogen bonds : angle 4.64534 ( 1272) SS BOND : bond 0.00122 ( 3) SS BOND : angle 1.07228 ( 6) covalent geometry : bond 0.00306 ( 8740) covalent geometry : angle 0.54731 (11917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.928 Fit side-chains REVERT: A 59 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7761 (mm-40) REVERT: A 331 ASP cc_start: 0.7645 (m-30) cc_final: 0.7432 (m-30) REVERT: B 171 ILE cc_start: 0.7370 (mm) cc_final: 0.7054 (mp) REVERT: B 188 MET cc_start: 0.8527 (mmm) cc_final: 0.8233 (mmp) REVERT: B 269 ILE cc_start: 0.8333 (pt) cc_final: 0.7949 (pp) REVERT: G 38 MET cc_start: 0.7666 (mtm) cc_final: 0.7375 (ttp) REVERT: S 85 SER cc_start: 0.8598 (t) cc_final: 0.8248 (p) REVERT: S 218 MET cc_start: 0.8562 (ttp) cc_final: 0.8252 (ttm) REVERT: R 106 TYR cc_start: 0.8549 (m-80) cc_final: 0.8018 (m-80) REVERT: R 132 PHE cc_start: 0.8166 (m-80) cc_final: 0.7753 (m-80) REVERT: R 249 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7550 (tp) outliers start: 17 outliers final: 12 residues processed: 216 average time/residue: 0.9809 time to fit residues: 228.7221 Evaluate side-chains 225 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 0.0670 chunk 18 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 119 ASN B 125 ASN R 179 GLN R 269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108330 restraints weight = 12647.126| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.54 r_work: 0.3439 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8743 Z= 0.146 Angle : 0.553 8.523 11923 Z= 0.296 Chirality : 0.042 0.142 1383 Planarity : 0.004 0.045 1511 Dihedral : 4.539 20.967 1230 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.76 % Allowed : 22.30 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.51 (0.26), residues: 1122 helix: 1.63 (0.28), residues: 388 sheet: 0.11 (0.30), residues: 288 loop : -0.60 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.001 PHE R 260 TYR 0.022 0.002 TYR R 268 ARG 0.009 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 445) hydrogen bonds : angle 4.65531 ( 1272) SS BOND : bond 0.00152 ( 3) SS BOND : angle 1.08393 ( 6) covalent geometry : bond 0.00334 ( 8740) covalent geometry : angle 0.55276 (11917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.899 Fit side-chains REVERT: A 331 ASP cc_start: 0.7632 (m-30) cc_final: 0.7419 (m-30) REVERT: B 171 ILE cc_start: 0.7473 (mm) cc_final: 0.7215 (mp) REVERT: B 269 ILE cc_start: 0.8338 (pt) cc_final: 0.7953 (pp) REVERT: G 38 MET cc_start: 0.7670 (mtm) cc_final: 0.7382 (ttp) REVERT: S 85 SER cc_start: 0.8597 (t) cc_final: 0.8241 (p) REVERT: S 132 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7550 (m) REVERT: S 218 MET cc_start: 0.8558 (ttp) cc_final: 0.8237 (ttm) REVERT: R 106 TYR cc_start: 0.8554 (m-80) cc_final: 0.8077 (m-80) REVERT: R 132 PHE cc_start: 0.8182 (m-80) cc_final: 0.7765 (m-80) REVERT: R 249 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7535 (tp) outliers start: 15 outliers final: 11 residues processed: 211 average time/residue: 1.0545 time to fit residues: 239.2366 Evaluate side-chains 216 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 43 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 294 GLN B 125 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107142 restraints weight = 12754.186| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.55 r_work: 0.3412 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8743 Z= 0.183 Angle : 0.581 8.328 11923 Z= 0.311 Chirality : 0.043 0.161 1383 Planarity : 0.004 0.045 1511 Dihedral : 4.638 20.746 1230 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.64 % Allowed : 22.42 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.45 (0.26), residues: 1122 helix: 1.56 (0.28), residues: 388 sheet: 0.03 (0.30), residues: 284 loop : -0.56 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE R 265 TYR 0.022 0.002 TYR R 268 ARG 0.009 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 445) hydrogen bonds : angle 4.72913 ( 1272) SS BOND : bond 0.00165 ( 3) SS BOND : angle 1.21275 ( 6) covalent geometry : bond 0.00418 ( 8740) covalent geometry : angle 0.58059 (11917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7617.22 seconds wall clock time: 132 minutes 21.69 seconds (7941.69 seconds total)