Starting phenix.real_space_refine on Tue Mar 3 20:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sbf_24978/03_2026/7sbf_24978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbf_24978/03_2026/7sbf_24978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2026/7sbf_24978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2026/7sbf_24978.map" model { file = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2026/7sbf_24978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbf_24978/03_2026/7sbf_24978.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 65 5.16 5 C 5452 2.51 5 N 1450 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8525 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1683 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2537 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2157 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'8QY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.23 Number of scatterers: 8525 At special positions: 0 Unit cell: (98.58, 116.6, 115.54, 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 65 16.00 O 1558 8.00 N 1450 7.00 C 5452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 309.1 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.932A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.636A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.371A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.714A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.340A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.980A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.066A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.610A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.951A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.976A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.232A pdb=" N THR R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 120 removed outlier: 3.906A pdb=" N THR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 131 removed outlier: 3.548A pdb=" N GLN R 124 " --> pdb=" O THR R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 140 removed outlier: 3.978A pdb=" N LEU R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS R 140 " --> pdb=" O GLY R 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 135 through 140' Processing helix chain 'R' and resid 142 through 171 removed outlier: 3.617A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 179 removed outlier: 3.666A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 206 removed outlier: 3.714A pdb=" N ALA R 197 " --> pdb=" O ILE R 193 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 224 through 241 removed outlier: 4.748A pdb=" N ASN R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 260 removed outlier: 3.870A pdb=" N VAL R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 266 removed outlier: 6.767A pdb=" N MET R 264 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER R 266 " --> pdb=" O ARG R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 306 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 311 through 337 removed outlier: 3.772A pdb=" N THR R 315 " --> pdb=" O THR R 311 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.523A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.572A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.547A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.182A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.836A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.599A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.794A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.801A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.837A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.837A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.456A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 208 through 209 removed outlier: 3.583A pdb=" N ASP R 216 " --> pdb=" O LYS R 209 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2710 1.34 - 1.46: 1866 1.46 - 1.58: 4032 1.58 - 1.69: 3 1.69 - 1.81: 94 Bond restraints: 8705 Sorted by residual: bond pdb=" C02 8QY R 501 " pdb=" N03 8QY R 501 " ideal model delta sigma weight residual 1.365 1.441 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C02 8QY R 501 " pdb=" N12 8QY R 501 " ideal model delta sigma weight residual 1.360 1.423 -0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" N ILE R 142 " pdb=" CA ILE R 142 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" C04 8QY R 501 " pdb=" N03 8QY R 501 " ideal model delta sigma weight residual 1.449 1.500 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C13 8QY R 501 " pdb=" C14 8QY R 501 " ideal model delta sigma weight residual 1.536 1.586 -0.050 2.00e-02 2.50e+03 6.30e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11615 2.02 - 4.04: 171 4.04 - 6.06: 31 6.06 - 8.09: 6 8.09 - 10.11: 3 Bond angle restraints: 11826 Sorted by residual: angle pdb=" N LYS R 141 " pdb=" CA LYS R 141 " pdb=" C LYS R 141 " ideal model delta sigma weight residual 113.17 103.06 10.11 1.26e+00 6.30e-01 6.43e+01 angle pdb=" C ILE B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta sigma weight residual 121.14 114.16 6.98 1.75e+00 3.27e-01 1.59e+01 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.16 108.30 4.86 1.24e+00 6.50e-01 1.54e+01 angle pdb=" C ARG B 19 " pdb=" N ASP B 20 " pdb=" CA ASP B 20 " ideal model delta sigma weight residual 121.58 114.47 7.11 1.95e+00 2.63e-01 1.33e+01 angle pdb=" CA ILE R 142 " pdb=" C ILE R 142 " pdb=" O ILE R 142 " ideal model delta sigma weight residual 120.78 116.33 4.45 1.25e+00 6.40e-01 1.27e+01 ... (remaining 11821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4715 17.74 - 35.48: 366 35.48 - 53.23: 36 53.23 - 70.97: 10 70.97 - 88.71: 7 Dihedral angle restraints: 5134 sinusoidal: 1883 harmonic: 3251 Sorted by residual: dihedral pdb=" CB CYS R 140 " pdb=" SG CYS R 140 " pdb=" SG CYS R 217 " pdb=" CB CYS R 217 " ideal model delta sinusoidal sigma weight residual -86.00 -162.14 76.14 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER R 268 " pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta harmonic sigma weight residual 180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1171 0.065 - 0.131: 192 0.131 - 0.196: 6 0.196 - 0.261: 0 0.261 - 0.327: 3 Chirality restraints: 1372 Sorted by residual: chirality pdb=" C14 8QY R 501 " pdb=" C13 8QY R 501 " pdb=" C15 8QY R 501 " pdb=" N23 8QY R 501 " both_signs ideal model delta sigma weight residual False 2.36 2.69 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASP B 247 " pdb=" N ASP B 247 " pdb=" C ASP B 247 " pdb=" CB ASP B 247 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA LYS R 141 " pdb=" N LYS R 141 " pdb=" C LYS R 141 " pdb=" CB LYS R 141 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1369 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 308 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO R 309 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 309 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 309 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 83 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU R 83 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU R 83 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE R 84 " -0.011 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 724 2.74 - 3.28: 8503 3.28 - 3.82: 14213 3.82 - 4.36: 17111 4.36 - 4.90: 30122 Nonbonded interactions: 70673 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.200 3.040 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.244 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.268 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.299 3.120 ... (remaining 70668 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: 0.700 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.005 0.082 8708 Z= 0.218 Angle : 0.652 10.106 11832 Z= 0.357 Chirality : 0.047 0.327 1372 Planarity : 0.004 0.058 1485 Dihedral : 12.821 88.712 3027 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 0.23 % Allowed : 0.68 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1103 helix: 0.92 (0.28), residues: 367 sheet: -0.37 (0.28), residues: 289 loop : -0.41 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.017 0.002 TYR A 296 PHE 0.015 0.001 PHE A 274 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8705) covalent geometry : angle 0.65198 (11826) SS BOND : bond 0.00401 ( 3) SS BOND : angle 1.05217 ( 6) hydrogen bonds : bond 0.13156 ( 429) hydrogen bonds : angle 6.76638 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7139 (mp0) cc_final: 0.6905 (mp0) REVERT: A 247 MET cc_start: 0.8579 (mtp) cc_final: 0.8330 (mtp) REVERT: A 273 LEU cc_start: 0.8744 (tp) cc_final: 0.8522 (tm) REVERT: A 308 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 337 ASP cc_start: 0.7884 (m-30) cc_final: 0.7655 (m-30) REVERT: R 86 ASN cc_start: 0.7868 (m-40) cc_final: 0.7657 (m-40) REVERT: R 87 PHE cc_start: 0.8036 (m-10) cc_final: 0.7422 (m-80) REVERT: R 190 CYS cc_start: 0.8128 (t) cc_final: 0.7829 (t) REVERT: R 342 ASN cc_start: 0.7970 (m-40) cc_final: 0.7715 (m-40) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.5498 time to fit residues: 111.2334 Evaluate side-chains 144 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 256 ASN B 268 ASN C 59 ASN E 167 GLN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104438 restraints weight = 11939.419| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.48 r_work: 0.3151 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8708 Z= 0.133 Angle : 0.561 8.087 11832 Z= 0.295 Chirality : 0.043 0.136 1372 Planarity : 0.003 0.044 1485 Dihedral : 6.317 89.642 1221 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.04 % Allowed : 14.16 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1103 helix: 1.15 (0.28), residues: 365 sheet: -0.30 (0.29), residues: 277 loop : -0.37 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.016 0.001 TYR A 296 PHE 0.012 0.001 PHE R 135 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 297 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8705) covalent geometry : angle 0.56107 (11826) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.09000 ( 6) hydrogen bonds : bond 0.03880 ( 429) hydrogen bonds : angle 5.10564 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.341 Fit side-chains REVERT: A 14 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: A 242 ARG cc_start: 0.7291 (mmp-170) cc_final: 0.7042 (mmp-170) REVERT: A 245 GLU cc_start: 0.7432 (mp0) cc_final: 0.6941 (mp0) REVERT: A 247 MET cc_start: 0.8841 (mtp) cc_final: 0.8630 (mtp) REVERT: A 337 ASP cc_start: 0.8385 (m-30) cc_final: 0.8092 (m-30) REVERT: B 42 ARG cc_start: 0.7548 (tpt170) cc_final: 0.7242 (tpp-160) REVERT: E 84 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9105 (p) REVERT: R 87 PHE cc_start: 0.8270 (m-10) cc_final: 0.7784 (m-80) REVERT: R 130 MET cc_start: 0.8071 (mpp) cc_final: 0.7726 (mpp) REVERT: R 258 ARG cc_start: 0.8019 (tmt170) cc_final: 0.7755 (tmt170) outliers start: 18 outliers final: 10 residues processed: 167 average time/residue: 0.5929 time to fit residues: 104.8048 Evaluate side-chains 158 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.0570 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 306 GLN B 13 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN C 59 ASN E 182 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 ASN ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107766 restraints weight = 11808.864| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.48 r_work: 0.3199 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8708 Z= 0.103 Angle : 0.522 7.422 11832 Z= 0.274 Chirality : 0.042 0.129 1372 Planarity : 0.003 0.045 1485 Dihedral : 5.987 87.145 1221 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.38 % Allowed : 17.44 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1103 helix: 1.18 (0.27), residues: 373 sheet: -0.16 (0.29), residues: 278 loop : -0.44 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.015 0.001 TYR R 149 PHE 0.010 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.001 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8705) covalent geometry : angle 0.52203 (11826) SS BOND : bond 0.00128 ( 3) SS BOND : angle 1.04369 ( 6) hydrogen bonds : bond 0.03388 ( 429) hydrogen bonds : angle 4.70788 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: A 20 ASP cc_start: 0.8444 (t0) cc_final: 0.8169 (m-30) REVERT: A 245 GLU cc_start: 0.7449 (mp0) cc_final: 0.6823 (mp0) REVERT: A 273 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 337 ASP cc_start: 0.8358 (m-30) cc_final: 0.8087 (m-30) REVERT: B 42 ARG cc_start: 0.7654 (tpt170) cc_final: 0.7372 (tpp-160) REVERT: B 172 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8495 (tp30) REVERT: E 43 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8292 (mmmt) REVERT: E 171 GLN cc_start: 0.8559 (mt0) cc_final: 0.8257 (mt0) REVERT: R 65 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7153 (tt) REVERT: R 87 PHE cc_start: 0.8273 (m-10) cc_final: 0.7773 (m-80) REVERT: R 124 GLN cc_start: 0.7570 (mp10) cc_final: 0.7267 (mp10) REVERT: R 130 MET cc_start: 0.8016 (mpp) cc_final: 0.7681 (mpp) REVERT: R 258 ARG cc_start: 0.8056 (tmt170) cc_final: 0.7809 (tmt170) outliers start: 21 outliers final: 6 residues processed: 177 average time/residue: 0.5423 time to fit residues: 101.9233 Evaluate side-chains 160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 306 GLN B 13 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.140529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103773 restraints weight = 11972.970| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.52 r_work: 0.3133 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8708 Z= 0.173 Angle : 0.567 8.723 11832 Z= 0.296 Chirality : 0.043 0.140 1372 Planarity : 0.003 0.047 1485 Dihedral : 5.905 83.961 1221 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.17 % Allowed : 18.46 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1103 helix: 1.41 (0.28), residues: 360 sheet: -0.14 (0.29), residues: 287 loop : -0.49 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.018 0.002 TYR A 296 PHE 0.011 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8705) covalent geometry : angle 0.56613 (11826) SS BOND : bond 0.00169 ( 3) SS BOND : angle 1.56526 ( 6) hydrogen bonds : bond 0.03723 ( 429) hydrogen bonds : angle 4.79132 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: A 20 ASP cc_start: 0.8520 (t0) cc_final: 0.8230 (m-30) REVERT: A 245 GLU cc_start: 0.7642 (mp0) cc_final: 0.7119 (mp0) REVERT: A 308 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 337 ASP cc_start: 0.8389 (m-30) cc_final: 0.8072 (m-30) REVERT: B 42 ARG cc_start: 0.7661 (tpt170) cc_final: 0.7356 (tpp-160) REVERT: B 156 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: B 172 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8528 (tp30) REVERT: E 43 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8298 (mmmm) REVERT: R 65 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7152 (tt) REVERT: R 87 PHE cc_start: 0.8328 (m-10) cc_final: 0.7843 (m-80) REVERT: R 258 ARG cc_start: 0.8017 (tmt170) cc_final: 0.7740 (tmt170) outliers start: 28 outliers final: 10 residues processed: 169 average time/residue: 0.5577 time to fit residues: 100.0289 Evaluate side-chains 160 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 HIS ** R 332 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 = 0.3802 r_free = 0.3802 target = 0.140645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104097 restraints weight = 12000.174| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.51 r_work: 0.3140 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8708 Z= 0.161 Angle : 0.555 9.116 11832 Z= 0.292 Chirality : 0.043 0.140 1372 Planarity : 0.003 0.047 1485 Dihedral : 5.762 80.365 1221 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.94 % Allowed : 19.37 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1103 helix: 1.54 (0.28), residues: 355 sheet: -0.14 (0.29), residues: 281 loop : -0.48 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.021 0.001 TYR A 230 PHE 0.012 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8705) covalent geometry : angle 0.55429 (11826) SS BOND : bond 0.00230 ( 3) SS BOND : angle 1.35460 ( 6) hydrogen bonds : bond 0.03644 ( 429) hydrogen bonds : angle 4.73127 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: A 20 ASP cc_start: 0.8487 (t0) cc_final: 0.8199 (m-30) REVERT: A 33 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: A 242 ARG cc_start: 0.7341 (mmp-170) cc_final: 0.6986 (mmp-170) REVERT: A 245 GLU cc_start: 0.7766 (mp0) cc_final: 0.7175 (mp0) REVERT: A 308 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 337 ASP cc_start: 0.8397 (m-30) cc_final: 0.8084 (m-30) REVERT: B 161 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8969 (t) REVERT: E 38 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8398 (ptp90) REVERT: E 43 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8321 (mmmm) REVERT: R 65 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7151 (tt) REVERT: R 87 PHE cc_start: 0.8341 (m-10) cc_final: 0.7880 (m-80) REVERT: R 258 ARG cc_start: 0.8045 (tmt170) cc_final: 0.7765 (tmt170) outliers start: 26 outliers final: 14 residues processed: 170 average time/residue: 0.5841 time to fit residues: 105.0392 Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105029 restraints weight = 11833.274| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.48 r_work: 0.3148 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8708 Z= 0.141 Angle : 0.543 9.479 11832 Z= 0.285 Chirality : 0.042 0.137 1372 Planarity : 0.003 0.047 1485 Dihedral : 5.583 76.289 1221 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.28 % Allowed : 20.27 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1103 helix: 1.59 (0.28), residues: 355 sheet: -0.13 (0.30), residues: 281 loop : -0.47 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.027 0.002 TYR A 230 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8705) covalent geometry : angle 0.54271 (11826) SS BOND : bond 0.00238 ( 3) SS BOND : angle 1.27855 ( 6) hydrogen bonds : bond 0.03509 ( 429) hydrogen bonds : angle 4.64933 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: A 20 ASP cc_start: 0.8445 (t0) cc_final: 0.8163 (m-30) REVERT: A 33 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: A 245 GLU cc_start: 0.7728 (mp0) cc_final: 0.7133 (mp0) REVERT: A 308 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 337 ASP cc_start: 0.8368 (m-30) cc_final: 0.8060 (m-30) REVERT: B 42 ARG cc_start: 0.7640 (tpt170) cc_final: 0.7347 (tpp-160) REVERT: B 156 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: B 161 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.8978 (t) REVERT: B 172 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8581 (tp30) REVERT: E 38 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8352 (ptp90) REVERT: R 65 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7118 (tt) REVERT: R 87 PHE cc_start: 0.8242 (m-10) cc_final: 0.7783 (m-80) REVERT: R 205 MET cc_start: 0.7060 (ttt) cc_final: 0.6797 (ttt) REVERT: R 258 ARG cc_start: 0.8070 (tmt170) cc_final: 0.7798 (tmt170) REVERT: R 344 LYS cc_start: 0.7283 (mmmm) cc_final: 0.7033 (mmmm) outliers start: 29 outliers final: 13 residues processed: 175 average time/residue: 0.5812 time to fit residues: 107.8597 Evaluate side-chains 167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 59 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104201 restraints weight = 12045.196| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.50 r_work: 0.3139 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8708 Z= 0.160 Angle : 0.578 10.525 11832 Z= 0.301 Chirality : 0.043 0.139 1372 Planarity : 0.003 0.045 1485 Dihedral : 5.515 72.289 1221 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.74 % Allowed : 20.72 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1103 helix: 1.45 (0.28), residues: 362 sheet: -0.13 (0.29), residues: 288 loop : -0.45 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.028 0.002 TYR A 230 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8705) covalent geometry : angle 0.57751 (11826) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.29664 ( 6) hydrogen bonds : bond 0.03584 ( 429) hydrogen bonds : angle 4.67338 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: A 20 ASP cc_start: 0.8470 (t0) cc_final: 0.8176 (m-30) REVERT: A 33 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: A 53 MET cc_start: 0.7435 (mmt) cc_final: 0.7211 (mmm) REVERT: A 242 ARG cc_start: 0.7445 (mmt180) cc_final: 0.7195 (mmt180) REVERT: A 245 GLU cc_start: 0.7780 (mp0) cc_final: 0.7115 (mp0) REVERT: A 306 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: A 308 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 337 ASP cc_start: 0.8387 (m-30) cc_final: 0.8080 (m-30) REVERT: B 161 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8976 (t) REVERT: B 172 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8568 (tp30) REVERT: E 38 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8329 (ptp90) REVERT: R 65 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7124 (tt) REVERT: R 87 PHE cc_start: 0.8256 (m-10) cc_final: 0.7812 (m-80) REVERT: R 205 MET cc_start: 0.7136 (ttt) cc_final: 0.6868 (ttt) REVERT: R 258 ARG cc_start: 0.8078 (tmt170) cc_final: 0.7803 (tmt170) outliers start: 33 outliers final: 20 residues processed: 166 average time/residue: 0.5947 time to fit residues: 104.6471 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 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 = 0.3802 r_free = 0.3802 target = 0.140613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104198 restraints weight = 11838.921| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.47 r_work: 0.3140 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8708 Z= 0.164 Angle : 0.581 11.092 11832 Z= 0.302 Chirality : 0.043 0.139 1372 Planarity : 0.003 0.045 1485 Dihedral : 5.455 69.653 1221 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.28 % Allowed : 20.84 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1103 helix: 1.48 (0.28), residues: 361 sheet: -0.14 (0.29), residues: 288 loop : -0.45 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.022 0.002 TYR A 296 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8705) covalent geometry : angle 0.58039 (11826) SS BOND : bond 0.00285 ( 3) SS BOND : angle 1.28729 ( 6) hydrogen bonds : bond 0.03582 ( 429) hydrogen bonds : angle 4.67976 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: A 20 ASP cc_start: 0.8433 (t0) cc_final: 0.8136 (m-30) REVERT: A 33 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: A 53 MET cc_start: 0.7431 (mmt) cc_final: 0.7211 (mmm) REVERT: A 242 ARG cc_start: 0.7447 (mmt180) cc_final: 0.7176 (mmt180) REVERT: A 245 GLU cc_start: 0.7777 (mp0) cc_final: 0.7018 (mp0) REVERT: A 306 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: A 308 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 337 ASP cc_start: 0.8380 (m-30) cc_final: 0.8070 (m-30) REVERT: B 161 SER cc_start: 0.9344 (OUTLIER) cc_final: 0.8968 (t) REVERT: B 172 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8559 (tp30) REVERT: E 38 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8424 (ptp90) REVERT: R 65 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7110 (tt) REVERT: R 87 PHE cc_start: 0.8240 (m-10) cc_final: 0.7789 (m-80) REVERT: R 205 MET cc_start: 0.7146 (ttt) cc_final: 0.6875 (ttt) REVERT: R 258 ARG cc_start: 0.8065 (tmt170) cc_final: 0.7753 (tmt170) outliers start: 29 outliers final: 19 residues processed: 163 average time/residue: 0.5899 time to fit residues: 101.9551 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 70 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106805 restraints weight = 11894.531| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.51 r_work: 0.3181 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8708 Z= 0.114 Angle : 0.565 11.257 11832 Z= 0.292 Chirality : 0.042 0.129 1372 Planarity : 0.003 0.044 1485 Dihedral : 5.174 64.125 1221 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.49 % Allowed : 22.08 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1103 helix: 1.56 (0.28), residues: 362 sheet: -0.10 (0.30), residues: 280 loop : -0.47 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.025 0.001 TYR A 230 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP R 226 HIS 0.001 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8705) covalent geometry : angle 0.56453 (11826) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.50322 ( 6) hydrogen bonds : bond 0.03264 ( 429) hydrogen bonds : angle 4.51922 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: A 20 ASP cc_start: 0.8461 (t0) cc_final: 0.8157 (m-30) REVERT: A 33 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: A 53 MET cc_start: 0.7415 (mmt) cc_final: 0.7183 (mmm) REVERT: A 242 ARG cc_start: 0.7382 (mmt180) cc_final: 0.7125 (mmt180) REVERT: A 245 GLU cc_start: 0.7733 (mp0) cc_final: 0.7009 (mp0) REVERT: A 306 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: A 308 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8045 (mt-10) REVERT: A 337 ASP cc_start: 0.8311 (m-30) cc_final: 0.8036 (m-30) REVERT: R 65 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7080 (tt) REVERT: R 87 PHE cc_start: 0.8254 (m-10) cc_final: 0.7787 (m-80) REVERT: R 205 MET cc_start: 0.6954 (ttt) cc_final: 0.6631 (ttt) REVERT: R 258 ARG cc_start: 0.8065 (tmt170) cc_final: 0.7819 (tmt170) outliers start: 22 outliers final: 13 residues processed: 170 average time/residue: 0.5691 time to fit residues: 102.7756 Evaluate side-chains 165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 60 optimal weight: 0.0170 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107100 restraints weight = 11844.296| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.51 r_work: 0.3187 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8708 Z= 0.118 Angle : 0.578 11.589 11832 Z= 0.297 Chirality : 0.042 0.133 1372 Planarity : 0.003 0.045 1485 Dihedral : 4.979 58.210 1221 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.27 % Allowed : 22.99 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1103 helix: 1.62 (0.28), residues: 360 sheet: -0.04 (0.30), residues: 280 loop : -0.47 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.011 0.001 TYR E 178 PHE 0.010 0.001 PHE A 189 TRP 0.011 0.001 TRP R 226 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8705) covalent geometry : angle 0.57648 (11826) SS BOND : bond 0.00208 ( 3) SS BOND : angle 1.77339 ( 6) hydrogen bonds : bond 0.03228 ( 429) hydrogen bonds : angle 4.46918 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: A 20 ASP cc_start: 0.8463 (t0) cc_final: 0.8165 (m-30) REVERT: A 33 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: A 53 MET cc_start: 0.7392 (mmt) cc_final: 0.7173 (mmm) REVERT: A 242 ARG cc_start: 0.7425 (mmt180) cc_final: 0.7007 (mmp-170) REVERT: A 245 GLU cc_start: 0.7810 (mp0) cc_final: 0.7168 (mp0) REVERT: A 308 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8023 (mt-10) REVERT: A 337 ASP cc_start: 0.8315 (m-30) cc_final: 0.8037 (m-30) REVERT: B 42 ARG cc_start: 0.7551 (tpt170) cc_final: 0.7162 (tpp-160) REVERT: B 172 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8523 (tp30) REVERT: R 65 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7096 (tt) REVERT: R 87 PHE cc_start: 0.8239 (m-10) cc_final: 0.7768 (m-80) REVERT: R 258 ARG cc_start: 0.8083 (tmt170) cc_final: 0.7852 (tmt170) outliers start: 20 outliers final: 13 residues processed: 160 average time/residue: 0.5607 time to fit residues: 95.4141 Evaluate side-chains 162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106976 restraints weight = 11759.823| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.50 r_work: 0.3187 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8708 Z= 0.124 Angle : 0.586 11.303 11832 Z= 0.301 Chirality : 0.042 0.133 1372 Planarity : 0.003 0.045 1485 Dihedral : 4.826 51.674 1221 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.04 % Allowed : 22.99 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 1103 helix: 1.59 (0.28), residues: 364 sheet: -0.01 (0.30), residues: 280 loop : -0.51 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.025 0.001 TYR A 230 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8705) covalent geometry : angle 0.58507 (11826) SS BOND : bond 0.00246 ( 3) SS BOND : angle 1.65075 ( 6) hydrogen bonds : bond 0.03300 ( 429) hydrogen bonds : angle 4.49610 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.32 seconds wall clock time: 60 minutes 44.75 seconds (3644.75 seconds total)