Starting phenix.real_space_refine on Thu Jul 2 11:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sbf_24978/07_2026/7sbf_24978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbf_24978/07_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_24978/07_2026/7sbf_24978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2026/7sbf_24978.map" model { file = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2026/7sbf_24978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2026/7sbf_24978.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2026/7sbf_24978.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_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-6108/lib/python3.11/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: 2.10, per 1000 atoms: 0.25 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: 0.70 Conformation dependent library (CDL) restraints added in 530.8 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: 0.25 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: 1.40 Time building geometry restraints manager: 0.94 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: 4710 17.74 - 35.48: 361 35.48 - 53.23: 34 53.23 - 70.97: 10 70.97 - 88.71: 7 Dihedral angle restraints: 5122 sinusoidal: 1871 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 5119 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: 1.060 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 12.736 88.712 3015 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/Z covalent geometry : bond 0.00472 / 0.22 ( 8705) covalent geometry : angle 0.65198 / 0.36 (11826) SS BOND : bond 0.00401 / 0.20 ( 3) SS BOND : angle 1.05217 / 0.51 ( 6) hydrogen bonds : bond 0.13156 / 8.64 ( 429) hydrogen bonds : angle 6.76638 / 4.97 ( 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 : 0.347 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: 0.5417 time to fit residues: 109.9652 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 : 0.281 ------------------------------------------------------------------------------- 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... 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 = 0.3801 r_free = 0.3801 target = 0.140967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104502 restraints weight = 11937.843| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.48 r_work: 0.3152 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1192 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= 0.132 Angle : 0.559 8.113 11832 Z= 0.294 Chirality : 0.043 0.136 1372 Planarity : 0.003 0.044 1485 Dihedral : 5.731 87.143 1209 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.93 % Allowed : 14.27 % 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: 0.16 (0.25), residues: 1103 helix: 1.15 (0.28), residues: 365 sheet: -0.29 (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 42 TYR 0.016 0.001 TYR A 296 PHE 0.012 0.001 PHE R 135 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8705) covalent geometry : angle 0.55817 / 0.29 (11826) SS BOND : bond 0.00309 / 0.16 ( 3) SS BOND : angle 1.08365 / 0.49 ( 6) hydrogen bonds : bond 0.03874 / 2.61 ( 429) hydrogen bonds : angle 5.08610 / 3.66 ( 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 177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: A 242 ARG cc_start: 0.7288 (mmp-170) cc_final: 0.7038 (mmp-170) REVERT: A 245 GLU cc_start: 0.7433 (mp0) cc_final: 0.6936 (mp0) REVERT: A 247 MET cc_start: 0.8837 (mtp) cc_final: 0.8624 (mtp) REVERT: A 337 ASP cc_start: 0.8384 (m-30) cc_final: 0.8092 (m-30) REVERT: B 13 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8226 (pp30) REVERT: B 42 ARG cc_start: 0.7570 (tpt170) cc_final: 0.7270 (tpp-160) REVERT: E 84 THR cc_start: 0.9332 (m) cc_final: 0.9100 (p) REVERT: R 87 PHE cc_start: 0.8272 (m-10) cc_final: 0.7805 (m-80) REVERT: R 130 MET cc_start: 0.8069 (mpp) cc_final: 0.7703 (mpp) REVERT: R 258 ARG cc_start: 0.7983 (tmt170) cc_final: 0.7718 (tmt170) outliers start: 17 outliers final: 10 residues processed: 168 average time/residue: 0.5247 time to fit residues: 93.9022 Evaluate side-chains 159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.0370 chunk 14 optimal weight: 0.0470 chunk 8 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 306 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 328 ASN ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106861 restraints weight = 11818.307| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.48 r_work: 0.3184 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8708 Z= 0.110 Angle : 0.527 7.449 11832 Z= 0.276 Chirality : 0.042 0.131 1372 Planarity : 0.003 0.045 1485 Dihedral : 5.515 86.842 1209 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.49 % Allowed : 17.67 % Favored : 79.84 % 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: 0.21 (0.25), residues: 1103 helix: 1.19 (0.27), residues: 373 sheet: -0.17 (0.29), residues: 278 loop : -0.43 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.015 0.001 TYR R 149 PHE 0.011 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8705) covalent geometry : angle 0.52640 / 0.28 (11826) SS BOND : bond 0.00613 / 0.32 ( 3) SS BOND : angle 1.28097 / 0.67 ( 6) hydrogen bonds : bond 0.03447 / 2.33 ( 429) hydrogen bonds : angle 4.73912 / 3.39 ( 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 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: A 20 ASP cc_start: 0.8451 (t0) cc_final: 0.8169 (m-30) REVERT: A 242 ARG cc_start: 0.7280 (mmp-170) cc_final: 0.6971 (mmp-170) REVERT: A 245 GLU cc_start: 0.7457 (mp0) cc_final: 0.6765 (mp0) REVERT: A 273 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 337 ASP cc_start: 0.8355 (m-30) cc_final: 0.8056 (m-30) REVERT: B 13 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8206 (pp30) REVERT: B 42 ARG cc_start: 0.7663 (tpt170) cc_final: 0.7395 (tpp-160) REVERT: B 172 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8502 (tp30) REVERT: E 43 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8320 (mmmt) REVERT: E 171 GLN cc_start: 0.8565 (mt0) cc_final: 0.8256 (mt0) REVERT: R 65 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7165 (tt) REVERT: R 87 PHE cc_start: 0.8282 (m-10) cc_final: 0.7812 (m-80) REVERT: R 130 MET cc_start: 0.8010 (mpp) cc_final: 0.7678 (mpp) REVERT: R 258 ARG cc_start: 0.8035 (tmt170) cc_final: 0.7775 (tmt170) outliers start: 22 outliers final: 7 residues processed: 169 average time/residue: 0.5105 time to fit residues: 91.8064 Evaluate side-chains 159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.0020 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108403 restraints weight = 11960.127| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.49 r_work: 0.3220 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1859 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= 0.099 Angle : 0.510 7.678 11832 Z= 0.266 Chirality : 0.041 0.130 1372 Planarity : 0.003 0.045 1485 Dihedral : 5.320 85.294 1209 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.72 % Allowed : 18.23 % Favored : 79.05 % 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: 1.45 (0.28), residues: 364 sheet: -0.05 (0.29), residues: 280 loop : -0.43 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.021 0.001 TYR A 296 PHE 0.010 0.001 PHE A 189 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 8705) covalent geometry : angle 0.50912 / 0.27 (11826) SS BOND : bond 0.00134 / 0.07 ( 3) SS BOND : angle 1.17027 / 0.60 ( 6) hydrogen bonds : bond 0.03233 / 2.18 ( 429) hydrogen bonds : angle 4.54240 / 3.24 ( 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 196 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: A 18 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7884 (mtp) REVERT: A 20 ASP cc_start: 0.8407 (t0) cc_final: 0.8101 (m-30) REVERT: A 242 ARG cc_start: 0.7327 (mmp-170) cc_final: 0.7092 (mmt180) REVERT: A 245 GLU cc_start: 0.7565 (mp0) cc_final: 0.6878 (mp0) REVERT: A 308 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7997 (mt-10) REVERT: A 337 ASP cc_start: 0.8332 (m-30) cc_final: 0.8042 (m-30) REVERT: B 42 ARG cc_start: 0.7642 (tpt170) cc_final: 0.7358 (tpp-160) REVERT: B 172 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8496 (tp30) REVERT: R 65 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7134 (tt) REVERT: R 87 PHE cc_start: 0.8294 (m-10) cc_final: 0.7799 (m-80) REVERT: R 124 GLN cc_start: 0.7556 (mp10) cc_final: 0.7350 (mp10) REVERT: R 258 ARG cc_start: 0.8074 (tmt170) cc_final: 0.7847 (tmt170) outliers start: 24 outliers final: 8 residues processed: 181 average time/residue: 0.4534 time to fit residues: 87.2760 Evaluate side-chains 162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR 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: 0.6980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 188 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103145 restraints weight = 12014.040| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.51 r_work: 0.3121 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8708 Z= 0.200 Angle : 0.586 9.565 11832 Z= 0.307 Chirality : 0.044 0.135 1372 Planarity : 0.004 0.043 1485 Dihedral : 5.532 84.519 1209 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.85 % Allowed : 18.80 % Favored : 77.35 % 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: 0.35 (0.25), residues: 1103 helix: 1.41 (0.28), residues: 362 sheet: -0.10 (0.29), residues: 299 loop : -0.42 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.013 0.002 TYR A 302 PHE 0.011 0.001 PHE A 196 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 8705) covalent geometry : angle 0.58521 / 0.31 (11826) SS BOND : bond 0.00146 / 0.07 ( 3) SS BOND : angle 1.60534 / 0.83 ( 6) hydrogen bonds : bond 0.03800 / 2.55 ( 429) hydrogen bonds : angle 4.81680 / 3.45 ( 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 192 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: A 20 ASP cc_start: 0.8480 (t0) cc_final: 0.8182 (m-30) REVERT: A 33 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: A 188 HIS cc_start: 0.8324 (m90) cc_final: 0.7729 (t70) REVERT: A 245 GLU cc_start: 0.7680 (mp0) cc_final: 0.7185 (mp0) REVERT: A 306 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: A 308 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 337 ASP cc_start: 0.8387 (m-30) cc_final: 0.8006 (m-30) REVERT: B 161 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9002 (t) REVERT: E 38 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8313 (ptp90) REVERT: R 65 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7120 (tt) REVERT: R 87 PHE cc_start: 0.8365 (m-10) cc_final: 0.7864 (m-80) REVERT: R 258 ARG cc_start: 0.8023 (tmt170) cc_final: 0.7732 (tmt170) REVERT: R 343 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6616 (m-10) outliers start: 34 outliers final: 11 residues processed: 172 average time/residue: 0.5556 time to fit residues: 101.5412 Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 306 GLN Chi-restraints excluded: chain B residue 37 ILE 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 330 CYS Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103179 restraints weight = 11873.611| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.46 r_work: 0.3115 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8708 Z= 0.199 Angle : 0.590 10.248 11832 Z= 0.309 Chirality : 0.044 0.133 1372 Planarity : 0.004 0.044 1485 Dihedral : 5.556 84.585 1209 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.62 % Allowed : 20.27 % Favored : 76.10 % 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: 0.35 (0.26), residues: 1103 helix: 1.50 (0.28), residues: 356 sheet: -0.14 (0.29), residues: 299 loop : -0.43 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.022 0.002 TYR A 230 PHE 0.012 0.001 PHE A 307 TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 8705) covalent geometry : angle 0.58952 / 0.31 (11826) SS BOND : bond 0.00228 / 0.12 ( 3) SS BOND : angle 1.52054 / 0.78 ( 6) hydrogen bonds : bond 0.03804 / 2.55 ( 429) hydrogen bonds : angle 4.79966 / 3.44 ( 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 187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: A 20 ASP cc_start: 0.8491 (t0) cc_final: 0.8197 (m-30) REVERT: A 33 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: A 242 ARG cc_start: 0.7507 (mmt180) cc_final: 0.7234 (mmp-170) REVERT: A 245 GLU cc_start: 0.7714 (mp0) cc_final: 0.7019 (mp0) REVERT: A 308 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 337 ASP cc_start: 0.8389 (m-30) cc_final: 0.8067 (m-30) REVERT: B 161 SER cc_start: 0.9338 (OUTLIER) cc_final: 0.8983 (t) REVERT: E 38 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8341 (ptp90) REVERT: R 65 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7119 (tt) REVERT: R 87 PHE cc_start: 0.8242 (m-10) cc_final: 0.7803 (m-80) REVERT: R 258 ARG cc_start: 0.8032 (tmt170) cc_final: 0.7691 (tmt170) REVERT: R 343 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6610 (m-10) REVERT: R 344 LYS cc_start: 0.7214 (mmmm) cc_final: 0.7006 (mmmm) outliers start: 32 outliers final: 17 residues processed: 174 average time/residue: 0.6072 time to fit residues: 112.1832 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 276 GLU Chi-restraints excluded: chain A residue 285 ILE 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 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 Chi-restraints excluded: chain R residue 343 PHE 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: 0.9980 chunk 74 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104639 restraints weight = 12039.331| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.51 r_work: 0.3145 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8708 Z= 0.143 Angle : 0.571 10.451 11832 Z= 0.298 Chirality : 0.042 0.133 1372 Planarity : 0.003 0.044 1485 Dihedral : 5.436 83.967 1209 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.96 % Allowed : 20.72 % Favored : 75.31 % 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: 1.58 (0.28), residues: 356 sheet: -0.13 (0.30), residues: 282 loop : -0.44 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 42 TYR 0.029 0.001 TYR A 230 PHE 0.011 0.001 PHE A 274 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8705) covalent geometry : angle 0.57072 / 0.30 (11826) SS BOND : bond 0.00264 / 0.14 ( 3) SS BOND : angle 1.25973 / 0.64 ( 6) hydrogen bonds : bond 0.03544 / 2.38 ( 429) hydrogen bonds : angle 4.69359 / 3.36 ( 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 184 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: A 20 ASP cc_start: 0.8436 (t0) cc_final: 0.8137 (m-30) REVERT: A 33 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: A 242 ARG cc_start: 0.7490 (mmt180) cc_final: 0.7190 (mmp-170) REVERT: A 245 GLU cc_start: 0.7759 (mp0) cc_final: 0.7047 (mp0) REVERT: A 276 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: A 308 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8003 (mt-10) REVERT: A 337 ASP cc_start: 0.8380 (m-30) cc_final: 0.8073 (m-30) REVERT: E 38 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8284 (ptp90) REVERT: R 65 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7112 (tt) REVERT: R 87 PHE cc_start: 0.8252 (m-10) cc_final: 0.7804 (m-80) REVERT: R 258 ARG cc_start: 0.8077 (tmt170) cc_final: 0.7793 (tmt170) REVERT: R 343 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6606 (m-10) outliers start: 35 outliers final: 18 residues processed: 166 average time/residue: 0.6074 time to fit residues: 107.0172 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 198 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 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 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 Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.141028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104861 restraints weight = 11815.190| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.47 r_work: 0.3145 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8708 Z= 0.150 Angle : 0.584 11.080 11832 Z= 0.303 Chirality : 0.043 0.134 1372 Planarity : 0.003 0.044 1485 Dihedral : 5.396 83.118 1209 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.40 % Allowed : 21.52 % Favored : 75.08 % 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: 0.42 (0.26), residues: 1103 helix: 1.59 (0.28), residues: 356 sheet: -0.12 (0.30), residues: 288 loop : -0.40 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.022 0.001 TYR A 296 PHE 0.010 0.001 PHE A 189 TRP 0.013 0.001 TRP R 226 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8705) covalent geometry : angle 0.58270 / 0.30 (11826) SS BOND : bond 0.00244 / 0.12 ( 3) SS BOND : angle 1.97941 / 1.10 ( 6) hydrogen bonds : bond 0.03538 / 2.37 ( 429) hydrogen bonds : angle 4.66766 / 3.33 ( 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 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: A 20 ASP cc_start: 0.8426 (t0) cc_final: 0.8132 (m-30) REVERT: A 33 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: A 242 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7204 (mmp-170) REVERT: A 245 GLU cc_start: 0.7739 (mp0) cc_final: 0.6996 (mp0) REVERT: A 308 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 337 ASP cc_start: 0.8374 (m-30) cc_final: 0.8065 (m-30) REVERT: B 161 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.8969 (t) REVERT: R 65 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7107 (tt) REVERT: R 87 PHE cc_start: 0.8231 (m-10) cc_final: 0.7813 (m-80) REVERT: R 258 ARG cc_start: 0.8077 (tmt170) cc_final: 0.7805 (tmt170) REVERT: R 343 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6597 (m-10) REVERT: R 344 LYS cc_start: 0.7431 (mmmm) cc_final: 0.7225 (mmmm) outliers start: 30 outliers final: 19 residues processed: 167 average time/residue: 0.6014 time to fit residues: 106.6164 Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 198 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR 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 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 306 ILE Chi-restraints excluded: chain R residue 330 CYS Chi-restraints excluded: chain R residue 343 PHE 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: 1.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** 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 = 0.3832 r_free = 0.3832 target = 0.142941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106889 restraints weight = 11894.298| |-----------------------------------------------------------------------------| 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: 0.3048 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2130 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= 0.116 Angle : 0.567 11.175 11832 Z= 0.294 Chirality : 0.042 0.132 1372 Planarity : 0.003 0.043 1485 Dihedral : 5.194 80.582 1209 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.60 % Allowed : 23.22 % Favored : 74.18 % 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: 0.43 (0.26), residues: 1103 helix: 1.50 (0.28), residues: 363 sheet: -0.03 (0.30), residues: 279 loop : -0.40 (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 0.009 0.001 PHE A 189 TRP 0.012 0.001 TRP R 226 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8705) covalent geometry : angle 0.56600 / 0.29 (11826) SS BOND : bond 0.00204 / 0.10 ( 3) SS BOND : angle 1.83731 / 1.03 ( 6) hydrogen bonds : bond 0.03283 / 2.21 ( 429) hydrogen bonds : angle 4.52613 / 3.23 ( 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: 23 poor density : 158 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: A 20 ASP cc_start: 0.8455 (t0) cc_final: 0.8154 (m-30) REVERT: A 33 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: A 242 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7212 (mmp-170) REVERT: A 245 GLU cc_start: 0.7709 (mp0) cc_final: 0.7014 (mp0) REVERT: A 308 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 337 ASP cc_start: 0.8329 (m-30) cc_final: 0.8038 (m-30) REVERT: B 42 ARG cc_start: 0.7488 (tpt170) cc_final: 0.7184 (tpp-160) REVERT: R 65 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7087 (tt) REVERT: R 87 PHE cc_start: 0.8229 (m-10) cc_final: 0.7804 (m-80) REVERT: R 258 ARG cc_start: 0.8074 (tmt170) cc_final: 0.7835 (tmt170) REVERT: R 344 LYS cc_start: 0.7352 (mmmm) cc_final: 0.7140 (mmmm) outliers start: 23 outliers final: 14 residues processed: 169 average time/residue: 0.5669 time to fit residues: 101.8590 Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 316 THR 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 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 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 222 SER 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: 0.9980 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 109 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** 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 = 0.3813 r_free = 0.3813 target = 0.141258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105048 restraints weight = 11866.201| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.47 r_work: 0.3153 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8708 Z= 0.154 Angle : 0.595 11.787 11832 Z= 0.308 Chirality : 0.043 0.134 1372 Planarity : 0.003 0.045 1485 Dihedral : 5.244 79.771 1209 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.49 % Allowed : 23.67 % Favored : 73.84 % 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: 0.41 (0.26), residues: 1103 helix: 1.44 (0.28), residues: 366 sheet: -0.05 (0.30), residues: 280 loop : -0.38 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.016 0.001 TYR A 302 PHE 0.009 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 8705) covalent geometry : angle 0.59329 / 0.31 (11826) SS BOND : bond 0.00231 / 0.12 ( 3) SS BOND : angle 1.83990 / 1.02 ( 6) hydrogen bonds : bond 0.03489 / 2.34 ( 429) hydrogen bonds : angle 4.60990 / 3.29 ( 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 171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: A 20 ASP cc_start: 0.8503 (t0) cc_final: 0.8206 (m-30) REVERT: A 33 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: A 242 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7164 (mmp-170) REVERT: A 245 GLU cc_start: 0.7684 (mp0) cc_final: 0.6914 (mp0) REVERT: A 308 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8110 (mt-10) REVERT: A 337 ASP cc_start: 0.8367 (m-30) cc_final: 0.8056 (m-30) REVERT: B 42 ARG cc_start: 0.7638 (tpt170) cc_final: 0.7367 (tpp-160) REVERT: R 65 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7099 (tt) REVERT: R 87 PHE cc_start: 0.8236 (m-10) cc_final: 0.7812 (m-80) REVERT: R 186 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7309 (mp) REVERT: R 258 ARG cc_start: 0.8082 (tmt170) cc_final: 0.7832 (tmt170) REVERT: R 344 LYS cc_start: 0.7417 (mmmm) cc_final: 0.7201 (mmmm) outliers start: 22 outliers final: 15 residues processed: 162 average time/residue: 0.5812 time to fit residues: 100.1216 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 316 THR 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 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 145 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 222 SER 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: 0.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** 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 = 0.3776 r_free = 0.3776 target = 0.138346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102222 restraints weight = 11862.191| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.47 r_work: 0.3110 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8708 Z= 0.229 Angle : 0.653 11.893 11832 Z= 0.338 Chirality : 0.044 0.133 1372 Planarity : 0.004 0.046 1485 Dihedral : 5.470 78.811 1209 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.83 % Allowed : 23.44 % Favored : 73.73 % 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: 0.32 (0.26), residues: 1103 helix: 1.35 (0.28), residues: 363 sheet: -0.13 (0.29), residues: 298 loop : -0.38 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.027 0.002 TYR A 230 PHE 0.012 0.001 PHE A 196 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 ( 8705) covalent geometry : angle 0.65079 / 0.34 (11826) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 2.29095 / 1.27 ( 6) hydrogen bonds : bond 0.03904 / 2.60 ( 429) hydrogen bonds : angle 4.84248 / 3.47 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3493.95 seconds wall clock time: 60 minutes 26.13 seconds (3626.13 seconds total)