Starting phenix.real_space_refine on Sat Aug 23 03:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijd_60628/08_2025/9ijd_60628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijd_60628/08_2025/9ijd_60628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijd_60628/08_2025/9ijd_60628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijd_60628/08_2025/9ijd_60628.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijd_60628/08_2025/9ijd_60628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijd_60628/08_2025/9ijd_60628.cif" } resolution = 2.76 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= -0.001 sd= 0.098 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 60 5.16 5 C 5953 2.51 5 N 1628 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9371 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1893 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1808 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'CAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.37, per 1000 atoms: 0.25 Number of scatterers: 9371 At special positions: 0 Unit cell: (86.6, 122.322, 124.487, 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 60 16.00 O 1730 8.00 N 1628 7.00 C 5953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " distance=2.06 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: 0.92 Conformation dependent library (CDL) restraints added in 376.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 35.5% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 removed outlier: 4.082A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.764A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.695A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.845A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.966A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 65 Processing helix chain 'R' and resid 71 through 90 removed outlier: 3.972A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 removed outlier: 3.621A pdb=" N ALA R 94 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 141 removed outlier: 4.088A pdb=" N GLU R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU R 112 " --> pdb=" O THR R 108 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 149 removed outlier: 4.810A pdb=" N ALA R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 171 Processing helix chain 'R' and resid 202 through 213 Processing helix chain 'R' and resid 213 through 243 Processing helix chain 'R' and resid 290 through 319 removed outlier: 3.580A pdb=" N PHE R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) Proline residue: R 307 - end of helix removed outlier: 3.847A pdb=" N VAL R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 347 removed outlier: 3.802A pdb=" N ALA R 337 " --> pdb=" O TRP R 333 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 3.521A pdb=" N CYS R 347 " --> pdb=" O PRO R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 362 removed outlier: 4.007A pdb=" N ARG R 362 " --> pdb=" O ARG R 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.728A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.628A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.787A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 274 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 275 " --> pdb=" O LEU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.315A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.717A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.743A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.827A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.920A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.680A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.405A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.592A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.512A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.943A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.152A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 148 removed outlier: 6.220A pdb=" N VAL D 147 " --> pdb=" O GLU D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 194 through 195 removed outlier: 6.503A pdb=" N TRP D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR D 190 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 174 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.335A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1350 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: 1.63 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1499 1.30 - 1.43: 2631 1.43 - 1.56: 5354 1.56 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9569 Sorted by residual: bond pdb=" C VAL B 187 " pdb=" O VAL B 187 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.17e-02 7.31e+03 2.44e+01 bond pdb=" C GLY R 335 " pdb=" O GLY R 335 " ideal model delta sigma weight residual 1.234 1.190 0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C TYR D 173 " pdb=" O TYR D 173 " ideal model delta sigma weight residual 1.235 1.195 0.041 1.26e-02 6.30e+03 1.05e+01 bond pdb=" N MET D 192 " pdb=" CA MET D 192 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.47e+00 bond pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.22e-02 6.72e+03 8.87e+00 ... (remaining 9564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12491 1.94 - 3.89: 452 3.89 - 5.83: 45 5.83 - 7.77: 9 7.77 - 9.72: 5 Bond angle restraints: 13002 Sorted by residual: angle pdb=" O LEU D 233 " pdb=" C LEU D 233 " pdb=" N GLU D 234 " ideal model delta sigma weight residual 122.03 130.13 -8.10 1.04e+00 9.25e-01 6.07e+01 angle pdb=" N ASN R 332 " pdb=" CA ASN R 332 " pdb=" C ASN R 332 " ideal model delta sigma weight residual 111.82 104.58 7.24 1.16e+00 7.43e-01 3.89e+01 angle pdb=" C PRO A 316 " pdb=" CA PRO A 316 " pdb=" CB PRO A 316 " ideal model delta sigma weight residual 110.95 102.91 8.04 1.31e+00 5.83e-01 3.76e+01 angle pdb=" CA LEU D 233 " pdb=" C LEU D 233 " pdb=" N GLU D 234 " ideal model delta sigma weight residual 116.92 110.53 6.39 1.16e+00 7.43e-01 3.03e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.72 106.81 5.91 1.14e+00 7.69e-01 2.69e+01 ... (remaining 12997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 5300 27.07 - 54.15: 314 54.15 - 81.22: 32 81.22 - 108.29: 7 108.29 - 135.36: 2 Dihedral angle restraints: 5655 sinusoidal: 2115 harmonic: 3540 Sorted by residual: dihedral pdb=" CB CYS D 159 " pdb=" SG CYS D 159 " pdb=" SG CYS D 229 " pdb=" CB CYS D 229 " ideal model delta sinusoidal sigma weight residual 93.00 43.67 49.33 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -128.66 42.66 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" C PRO A 316 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " pdb=" CB PRO A 316 " ideal model delta harmonic sigma weight residual -120.70 -109.41 -11.29 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 5652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1258 0.070 - 0.140: 202 0.140 - 0.210: 23 0.210 - 0.280: 2 0.280 - 0.350: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA ARG D 98 " pdb=" N ARG D 98 " pdb=" C ARG D 98 " pdb=" CB ARG D 98 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA GLU D 234 " pdb=" N GLU D 234 " pdb=" C GLU D 234 " pdb=" CB GLU D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU B 10 " pdb=" N GLU B 10 " pdb=" C GLU B 10 " pdb=" CB GLU B 10 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1483 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 245 " -0.021 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C SER B 245 " 0.080 2.00e-02 2.50e+03 pdb=" O SER B 245 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP B 246 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 233 " -0.017 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C LEU D 233 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 233 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU D 234 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 98 " 0.252 9.50e-02 1.11e+02 1.13e-01 7.79e+00 pdb=" NE ARG D 98 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 98 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 98 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 98 " 0.009 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 608 2.72 - 3.27: 9454 3.27 - 3.81: 15993 3.81 - 4.36: 19900 4.36 - 4.90: 34367 Nonbonded interactions: 80322 Sorted by model distance: nonbonded pdb=" OD1 ASP D 109 " pdb=" N PHE D 110 " model vdw 2.181 3.120 nonbonded pdb=" O SER R 115 " pdb=" OG SER R 169 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.214 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.232 3.040 nonbonded pdb=" O TYR D 235 " pdb=" N LEU D 237 " model vdw 2.239 3.120 ... (remaining 80317 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: 0.760 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: 0.030 Set scattering table: 0.010 Process input model: 9.890 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: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.006 0.070 9573 Z= 0.373 Angle : 0.884 43.862 13010 Z= 0.546 Chirality : 0.052 0.350 1486 Planarity : 0.008 0.113 1653 Dihedral : 16.984 135.364 3365 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 1.73 % Allowed : 26.27 % Favored : 72.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.20 (0.24), residues: 1207 helix: 1.15 (0.26), residues: 364 sheet: -0.03 (0.29), residues: 312 loop : -0.37 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 160 TYR 0.021 0.002 TYR N 60 PHE 0.010 0.001 PHE A 212 TRP 0.016 0.002 TRP R 333 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 9569) covalent geometry : angle 0.77839 (13002) SS BOND : bond 0.01341 ( 4) SS BOND : angle 16.92447 ( 8) hydrogen bonds : bond 0.15762 ( 478) hydrogen bonds : angle 7.20646 ( 1350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.368 Fit side-chains REVERT: B 170 ASP cc_start: 0.6678 (t70) cc_final: 0.6467 (t70) REVERT: B 220 GLN cc_start: 0.7958 (mt0) cc_final: 0.7732 (mt0) REVERT: D 18 ARG cc_start: 0.6164 (tpp80) cc_final: 0.5879 (tpp80) outliers start: 17 outliers final: 10 residues processed: 211 average time/residue: 0.5160 time to fit residues: 116.6354 Evaluate side-chains 182 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 352 PHE Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.154895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114270 restraints weight = 12472.297| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.42 r_work: 0.3318 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9573 Z= 0.166 Angle : 0.570 7.467 13010 Z= 0.302 Chirality : 0.043 0.251 1486 Planarity : 0.005 0.071 1653 Dihedral : 6.988 114.339 1356 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.79 % Allowed : 26.17 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.51 (0.24), residues: 1207 helix: 1.73 (0.26), residues: 365 sheet: -0.07 (0.28), residues: 307 loop : -0.30 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.016 0.002 TYR D 235 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9569) covalent geometry : angle 0.56926 (13002) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.01607 ( 8) hydrogen bonds : bond 0.04631 ( 478) hydrogen bonds : angle 5.54100 ( 1350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 220 GLN cc_start: 0.8042 (mt0) cc_final: 0.7752 (mt0) REVERT: B 228 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: B 266 HIS cc_start: 0.8766 (t-90) cc_final: 0.8527 (t-90) REVERT: N 28 THR cc_start: 0.8058 (p) cc_final: 0.7747 (p) REVERT: N 95 TYR cc_start: 0.8308 (m-80) cc_final: 0.7730 (m-80) REVERT: N 108 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7360 (t80) REVERT: D 191 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7766 (mpt-90) REVERT: R 71 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7535 (tmm) REVERT: A 222 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7121 (p90) outliers start: 47 outliers final: 25 residues processed: 202 average time/residue: 0.4997 time to fit residues: 108.3900 Evaluate side-chains 191 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 352 PHE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 237 ASN B 340 ASN N 39 GLN R 73 ASN R 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116315 restraints weight = 12404.690| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.43 r_work: 0.3344 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9573 Z= 0.124 Angle : 0.518 6.355 13010 Z= 0.275 Chirality : 0.041 0.179 1486 Planarity : 0.004 0.061 1653 Dihedral : 6.199 94.123 1348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.80 % Allowed : 25.87 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.75 (0.24), residues: 1207 helix: 2.09 (0.27), residues: 365 sheet: -0.06 (0.29), residues: 306 loop : -0.20 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.011 0.001 TYR A 37 PHE 0.015 0.001 PHE A 212 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9569) covalent geometry : angle 0.51753 (13002) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.74742 ( 8) hydrogen bonds : bond 0.03962 ( 478) hydrogen bonds : angle 5.17123 ( 1350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 GLN cc_start: 0.8110 (mt0) cc_final: 0.7859 (mt0) REVERT: B 266 HIS cc_start: 0.8770 (t-90) cc_final: 0.8502 (t-90) REVERT: B 280 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7912 (mtpt) REVERT: B 312 ASP cc_start: 0.7890 (m-30) cc_final: 0.7447 (p0) REVERT: N 38 ARG cc_start: 0.8422 (ptt180) cc_final: 0.8154 (ptt180) REVERT: N 53 GLN cc_start: 0.8378 (mp10) cc_final: 0.8174 (mp10) REVERT: N 76 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8558 (mttp) REVERT: N 95 TYR cc_start: 0.8326 (m-80) cc_final: 0.7703 (m-80) REVERT: D 71 SER cc_start: 0.8674 (m) cc_final: 0.8018 (p) REVERT: D 191 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7363 (mpt-90) REVERT: R 71 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7590 (tmm) REVERT: R 155 ARG cc_start: 0.6777 (mtt180) cc_final: 0.5286 (mmt180) REVERT: A 222 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7190 (p90) REVERT: A 346 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6660 (mtm-85) outliers start: 57 outliers final: 21 residues processed: 211 average time/residue: 0.5382 time to fit residues: 121.9408 Evaluate side-chains 185 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN D 186 GLN R 73 ASN R 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112078 restraints weight = 12527.350| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.42 r_work: 0.3292 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9573 Z= 0.225 Angle : 0.595 8.853 13010 Z= 0.309 Chirality : 0.044 0.208 1486 Planarity : 0.005 0.066 1653 Dihedral : 6.172 97.669 1345 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.80 % Allowed : 25.76 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.55 (0.24), residues: 1207 helix: 1.77 (0.26), residues: 365 sheet: -0.07 (0.28), residues: 314 loop : -0.26 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 134 TYR 0.018 0.002 TYR N 80 PHE 0.016 0.002 PHE A 212 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 9569) covalent geometry : angle 0.59495 (13002) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.16724 ( 8) hydrogen bonds : bond 0.04647 ( 478) hydrogen bonds : angle 5.35950 ( 1350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: B 220 GLN cc_start: 0.8074 (mt0) cc_final: 0.7749 (mt0) REVERT: B 266 HIS cc_start: 0.8727 (t-90) cc_final: 0.8451 (t-90) REVERT: B 280 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7995 (mtpp) REVERT: N 53 GLN cc_start: 0.8222 (mp10) cc_final: 0.7987 (mp10) REVERT: N 76 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8540 (mttp) REVERT: N 95 TYR cc_start: 0.8264 (m-80) cc_final: 0.7683 (m-80) REVERT: D 98 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8251 (ptt180) REVERT: D 140 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8122 (mtp) REVERT: R 71 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7720 (tmm) REVERT: R 86 MET cc_start: 0.7546 (tpp) cc_final: 0.6950 (tpp) REVERT: R 155 ARG cc_start: 0.6889 (mtt180) cc_final: 0.5358 (mmt180) REVERT: A 222 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7103 (p90) REVERT: A 346 ARG cc_start: 0.6948 (mtm-85) cc_final: 0.6540 (mtm-85) outliers start: 57 outliers final: 33 residues processed: 201 average time/residue: 0.5254 time to fit residues: 113.5745 Evaluate side-chains 194 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN N 3 GLN N 39 GLN D 186 GLN R 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116134 restraints weight = 12497.908| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.42 r_work: 0.3343 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9573 Z= 0.120 Angle : 0.523 7.715 13010 Z= 0.275 Chirality : 0.042 0.176 1486 Planarity : 0.004 0.059 1653 Dihedral : 5.440 82.426 1343 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.28 % Allowed : 27.09 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.76 (0.24), residues: 1207 helix: 2.24 (0.27), residues: 359 sheet: -0.18 (0.28), residues: 310 loop : -0.19 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.012 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9569) covalent geometry : angle 0.52273 (13002) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.85664 ( 8) hydrogen bonds : bond 0.03832 ( 478) hydrogen bonds : angle 5.06901 ( 1350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7666 (mtt90) REVERT: B 59 TYR cc_start: 0.8912 (m-80) cc_final: 0.7272 (m-80) REVERT: B 266 HIS cc_start: 0.8741 (t-90) cc_final: 0.8373 (t-90) REVERT: B 280 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7820 (mtpm) REVERT: B 312 ASP cc_start: 0.8019 (m-30) cc_final: 0.7787 (m-30) REVERT: B 333 ASP cc_start: 0.7875 (p0) cc_final: 0.7505 (p0) REVERT: N 3 GLN cc_start: 0.7419 (tp40) cc_final: 0.7161 (tp40) REVERT: N 38 ARG cc_start: 0.8407 (ptt180) cc_final: 0.8130 (ptt180) REVERT: N 76 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8566 (mttp) REVERT: N 95 TYR cc_start: 0.8293 (m-80) cc_final: 0.7721 (m-80) REVERT: R 86 MET cc_start: 0.7692 (tpp) cc_final: 0.7063 (tpp) REVERT: R 155 ARG cc_start: 0.6588 (mtt180) cc_final: 0.5211 (mmt180) REVERT: A 222 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7038 (p90) REVERT: A 346 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6601 (mtm-85) outliers start: 42 outliers final: 24 residues processed: 193 average time/residue: 0.5125 time to fit residues: 105.7145 Evaluate side-chains 185 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 65 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 39 GLN D 142 GLN A 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114907 restraints weight = 12513.287| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.42 r_work: 0.3311 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9573 Z= 0.158 Angle : 0.554 8.386 13010 Z= 0.288 Chirality : 0.042 0.178 1486 Planarity : 0.004 0.063 1653 Dihedral : 5.477 82.931 1343 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.79 % Allowed : 27.39 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.68 (0.24), residues: 1207 helix: 2.13 (0.26), residues: 359 sheet: -0.23 (0.28), residues: 322 loop : -0.20 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 67 TYR 0.015 0.002 TYR N 80 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9569) covalent geometry : angle 0.55347 (13002) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.99134 ( 8) hydrogen bonds : bond 0.04046 ( 478) hydrogen bonds : angle 5.11417 ( 1350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8947 (m-80) cc_final: 0.7239 (m-80) REVERT: B 134 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7774 (ptp90) REVERT: B 266 HIS cc_start: 0.8693 (t-90) cc_final: 0.8340 (t-90) REVERT: B 280 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7882 (mtpt) REVERT: N 34 MET cc_start: 0.8516 (mmm) cc_final: 0.8089 (mmm) REVERT: N 38 ARG cc_start: 0.8293 (ptt180) cc_final: 0.7966 (ptt180) REVERT: N 95 TYR cc_start: 0.8236 (m-80) cc_final: 0.7691 (m-80) REVERT: R 86 MET cc_start: 0.7695 (tpp) cc_final: 0.6981 (tpp) REVERT: R 155 ARG cc_start: 0.6580 (mtt180) cc_final: 0.5228 (mmt180) REVERT: A 222 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.6999 (p90) REVERT: A 346 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6715 (mtm-85) outliers start: 47 outliers final: 31 residues processed: 190 average time/residue: 0.5039 time to fit residues: 102.6734 Evaluate side-chains 182 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN N 3 GLN N 39 GLN D 142 GLN D 186 GLN R 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116677 restraints weight = 12461.223| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.41 r_work: 0.3334 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9573 Z= 0.124 Angle : 0.540 10.186 13010 Z= 0.278 Chirality : 0.042 0.166 1486 Planarity : 0.004 0.061 1653 Dihedral : 5.217 73.175 1343 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.48 % Allowed : 28.92 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.78 (0.24), residues: 1207 helix: 2.29 (0.26), residues: 359 sheet: -0.17 (0.28), residues: 318 loop : -0.20 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 67 TYR 0.011 0.001 TYR A 348 PHE 0.015 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9569) covalent geometry : angle 0.53952 (13002) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.76759 ( 8) hydrogen bonds : bond 0.03736 ( 478) hydrogen bonds : angle 5.00124 ( 1350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7596 (mtt90) REVERT: B 59 TYR cc_start: 0.8834 (m-80) cc_final: 0.7174 (m-80) REVERT: B 228 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: B 266 HIS cc_start: 0.8709 (t-90) cc_final: 0.8357 (t-90) REVERT: B 280 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7829 (mtpm) REVERT: B 325 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7804 (tpp) REVERT: N 38 ARG cc_start: 0.8330 (ptt180) cc_final: 0.7940 (ptt180) REVERT: N 95 TYR cc_start: 0.8307 (m-80) cc_final: 0.7753 (m-80) REVERT: R 86 MET cc_start: 0.7698 (tpp) cc_final: 0.6920 (tpp) REVERT: R 155 ARG cc_start: 0.6414 (mtt180) cc_final: 0.5171 (mmt180) REVERT: A 222 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.6954 (p90) REVERT: A 346 ARG cc_start: 0.7021 (mtm-85) cc_final: 0.6697 (mtm-85) outliers start: 44 outliers final: 29 residues processed: 195 average time/residue: 0.5538 time to fit residues: 115.7616 Evaluate side-chains 189 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 156 GLN B 220 GLN B 237 ASN N 3 GLN N 39 GLN D 186 GLN R 141 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117535 restraints weight = 12355.095| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.40 r_work: 0.3360 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9573 Z= 0.117 Angle : 0.537 10.788 13010 Z= 0.277 Chirality : 0.042 0.155 1486 Planarity : 0.004 0.063 1653 Dihedral : 5.103 67.989 1343 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.48 % Allowed : 29.02 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.82 (0.24), residues: 1207 helix: 2.36 (0.26), residues: 359 sheet: -0.16 (0.28), residues: 318 loop : -0.20 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.013 0.001 TYR N 80 PHE 0.014 0.001 PHE A 212 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9569) covalent geometry : angle 0.53663 (13002) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.69075 ( 8) hydrogen bonds : bond 0.03624 ( 478) hydrogen bonds : angle 4.97204 ( 1350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7618 (mtt90) REVERT: B 59 TYR cc_start: 0.8788 (m-80) cc_final: 0.7291 (m-80) REVERT: B 134 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7825 (ptt-90) REVERT: B 228 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: B 266 HIS cc_start: 0.8723 (t-90) cc_final: 0.8367 (t-90) REVERT: B 280 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7880 (mtpt) REVERT: B 325 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7859 (tpp) REVERT: N 38 ARG cc_start: 0.8385 (ptt180) cc_final: 0.7972 (ptt180) REVERT: N 95 TYR cc_start: 0.8350 (m-80) cc_final: 0.7770 (m-80) REVERT: R 86 MET cc_start: 0.7709 (tpp) cc_final: 0.6721 (tpp) REVERT: R 155 ARG cc_start: 0.6437 (mtt180) cc_final: 0.5190 (mmt180) REVERT: A 222 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.6956 (p90) REVERT: A 323 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7772 (mtp-110) REVERT: A 346 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6723 (mtm-85) outliers start: 44 outliers final: 27 residues processed: 196 average time/residue: 0.5123 time to fit residues: 107.6408 Evaluate side-chains 190 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 3 GLN N 39 GLN D 142 GLN R 141 ASN R 332 ASN A 35 GLN A 41 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114095 restraints weight = 12423.430| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.40 r_work: 0.3315 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9573 Z= 0.185 Angle : 0.590 12.359 13010 Z= 0.305 Chirality : 0.044 0.204 1486 Planarity : 0.005 0.062 1653 Dihedral : 5.385 75.452 1343 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.97 % Allowed : 30.45 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.62 (0.24), residues: 1207 helix: 2.09 (0.26), residues: 359 sheet: -0.30 (0.28), residues: 323 loop : -0.22 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.013 0.002 TYR D 228 PHE 0.014 0.001 PHE A 212 TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9569) covalent geometry : angle 0.58914 (13002) SS BOND : bond 0.00194 ( 4) SS BOND : angle 1.05221 ( 8) hydrogen bonds : bond 0.04206 ( 478) hydrogen bonds : angle 5.16505 ( 1350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 266 HIS cc_start: 0.8735 (t-90) cc_final: 0.8368 (t-90) REVERT: B 280 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7861 (mtpt) REVERT: N 38 ARG cc_start: 0.8261 (ptt180) cc_final: 0.7820 (ptt180) REVERT: N 76 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8507 (mttp) REVERT: N 95 TYR cc_start: 0.8289 (m-80) cc_final: 0.7666 (m-80) REVERT: R 155 ARG cc_start: 0.6438 (mtt180) cc_final: 0.5105 (mmt180) REVERT: A 222 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7056 (p90) REVERT: A 323 ARG cc_start: 0.8376 (mtm110) cc_final: 0.7880 (mtp-110) REVERT: A 346 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6728 (mtm-85) outliers start: 39 outliers final: 28 residues processed: 178 average time/residue: 0.5883 time to fit residues: 112.1785 Evaluate side-chains 181 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN N 3 GLN N 39 GLN D 142 GLN R 332 ASN A 29 GLN A 35 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115627 restraints weight = 12363.101| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.40 r_work: 0.3323 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9573 Z= 0.147 Angle : 0.564 11.588 13010 Z= 0.291 Chirality : 0.043 0.179 1486 Planarity : 0.004 0.061 1653 Dihedral : 5.280 72.826 1343 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.67 % Allowed : 30.86 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.67 (0.24), residues: 1207 helix: 2.17 (0.26), residues: 359 sheet: -0.28 (0.28), residues: 320 loop : -0.22 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.014 0.002 TYR N 80 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9569) covalent geometry : angle 0.56402 (13002) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.85367 ( 8) hydrogen bonds : bond 0.03928 ( 478) hydrogen bonds : angle 5.08433 ( 1350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7762 (mtt90) REVERT: B 59 TYR cc_start: 0.8877 (m-80) cc_final: 0.7662 (m-80) REVERT: B 170 ASP cc_start: 0.6891 (t70) cc_final: 0.6414 (t70) REVERT: B 255 LEU cc_start: 0.8546 (mt) cc_final: 0.8150 (mp) REVERT: B 280 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7852 (mtpt) REVERT: B 325 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7772 (tpp) REVERT: N 38 ARG cc_start: 0.8253 (ptt180) cc_final: 0.7834 (ptt180) REVERT: N 76 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8506 (mttp) REVERT: N 95 TYR cc_start: 0.8339 (m-80) cc_final: 0.7759 (m-80) REVERT: R 155 ARG cc_start: 0.6458 (mtt180) cc_final: 0.5195 (mmt180) REVERT: A 222 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6820 (p90) REVERT: A 323 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7870 (mtp-110) REVERT: A 346 ARG cc_start: 0.7037 (mtm-85) cc_final: 0.6697 (mtm-85) outliers start: 36 outliers final: 29 residues processed: 190 average time/residue: 0.5963 time to fit residues: 121.3710 Evaluate side-chains 188 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 292 CYS Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 222 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 73 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 3 GLN N 39 GLN D 142 GLN R 332 ASN A 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118317 restraints weight = 12344.632| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.39 r_work: 0.3365 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9573 Z= 0.115 Angle : 0.556 11.073 13010 Z= 0.285 Chirality : 0.042 0.160 1486 Planarity : 0.004 0.062 1653 Dihedral : 5.077 64.125 1343 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.05 % Allowed : 31.06 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.80 (0.24), residues: 1207 helix: 2.34 (0.27), residues: 360 sheet: -0.20 (0.28), residues: 318 loop : -0.19 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.011 0.001 TYR A 37 PHE 0.013 0.001 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9569) covalent geometry : angle 0.55562 (13002) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.72343 ( 8) hydrogen bonds : bond 0.03592 ( 478) hydrogen bonds : angle 4.98599 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4440.38 seconds wall clock time: 76 minutes 20.39 seconds (4580.39 seconds total)