Starting phenix.real_space_refine on Thu Jul 2 16:10:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zh_67430/07_2026/20zh_67430.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zh_67430/07_2026/20zh_67430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/20zh_67430/07_2026/20zh_67430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zh_67430/07_2026/20zh_67430.map" model { file = "/net/cci-nas-00/data/ceres_data/20zh_67430/07_2026/20zh_67430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zh_67430/07_2026/20zh_67430.cif" } resolution = 2.4 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= 0.002 sd= 0.014 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 61 5.16 5 C 5702 2.51 5 N 1525 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8953 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2399 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 1.60, per 1000 atoms: 0.18 Number of scatterers: 8953 At special positions: 0 Unit cell: (87.98, 122.01, 131.97, 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 61 16.00 O 1665 8.00 N 1525 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.49 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.35 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: 0.43 Conformation dependent library (CDL) restraints added in 298.3 milliseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.8% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.684A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.513A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.379A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 328 through 351 removed outlier: 4.385A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.700A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.219A 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 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.669A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 128 Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 199 Processing helix chain 'R' and resid 201 through 207 removed outlier: 3.927A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET R 207 " --> pdb=" O MET R 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 207' Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.824A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 272 Processing helix chain 'R' and resid 295 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 365 Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 370 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.948A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.550A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.650A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.447A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.528A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.723A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.109A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.515A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.963A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.112A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.281A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 209 through 211 477 hydrogen bonds defined for protein. 1341 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: 1.10 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1448 1.30 - 1.43: 2546 1.43 - 1.57: 5058 1.57 - 1.70: 1 1.70 - 1.83: 90 Bond restraints: 9143 Sorted by residual: bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.587 -0.203 2.10e-02 2.27e+03 9.33e+01 bond pdb=" CA SER D 181 " pdb=" CB SER D 181 " ideal model delta sigma weight residual 1.537 1.430 0.108 1.38e-02 5.25e+03 6.08e+01 bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.533 1.421 0.112 1.51e-02 4.39e+03 5.50e+01 bond pdb=" CG HIS B 142 " pdb=" CD2 HIS B 142 " ideal model delta sigma weight residual 1.354 1.288 0.066 1.10e-02 8.26e+03 3.64e+01 bond pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " ideal model delta sigma weight residual 1.326 1.265 0.061 1.10e-02 8.26e+03 3.07e+01 ... (remaining 9138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 10337 2.67 - 5.34: 1828 5.34 - 8.01: 182 8.01 - 10.68: 41 10.68 - 13.34: 6 Bond angle restraints: 12394 Sorted by residual: angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 113.30 99.96 13.34 1.34e+00 5.57e-01 9.92e+01 angle pdb=" NE ARG R 372 " pdb=" CZ ARG R 372 " pdb=" NH2 ARG R 372 " ideal model delta sigma weight residual 119.20 110.78 8.42 9.00e-01 1.23e+00 8.75e+01 angle pdb=" NE ARG A 205 " pdb=" CZ ARG A 205 " pdb=" NH2 ARG A 205 " ideal model delta sigma weight residual 119.20 110.79 8.41 9.00e-01 1.23e+00 8.74e+01 angle pdb=" N PRO D 188 " pdb=" CA PRO D 188 " pdb=" CB PRO D 188 " ideal model delta sigma weight residual 103.39 94.89 8.50 9.40e-01 1.13e+00 8.19e+01 angle pdb=" C ARG D 179 " pdb=" CA ARG D 179 " pdb=" CB ARG D 179 " ideal model delta sigma weight residual 111.80 124.92 -13.12 1.46e+00 4.69e-01 8.08e+01 ... (remaining 12389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 4892 15.54 - 31.07: 377 31.07 - 46.61: 97 46.61 - 62.15: 29 62.15 - 77.69: 8 Dihedral angle restraints: 5403 sinusoidal: 2065 harmonic: 3338 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 170.42 -77.42 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CD ARG R 90 " pdb=" NE ARG R 90 " pdb=" CZ ARG R 90 " pdb=" NH1 ARG R 90 " ideal model delta sinusoidal sigma weight residual 0.00 -70.75 70.75 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" C LEU R 363 " pdb=" N LEU R 363 " pdb=" CA LEU R 363 " pdb=" CB LEU R 363 " ideal model delta harmonic sigma weight residual -122.60 -141.25 18.65 0 2.50e+00 1.60e-01 5.56e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1119 0.150 - 0.300: 250 0.300 - 0.449: 38 0.449 - 0.599: 6 0.599 - 0.749: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA LEU R 363 " pdb=" N LEU R 363 " pdb=" C LEU R 363 " pdb=" CB LEU R 363 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CA GLN R 269 " pdb=" N GLN R 269 " pdb=" C GLN R 269 " pdb=" CB GLN R 269 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" CA ASP R 149 " pdb=" N ASP R 149 " pdb=" C ASP R 149 " pdb=" CB ASP R 149 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.10e+00 ... (remaining 1412 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 205 " -0.785 9.50e-02 1.11e+02 3.58e-01 1.32e+02 pdb=" NE ARG A 205 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 205 " 0.139 2.00e-02 2.50e+03 pdb=" NH1 ARG A 205 " -0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG A 205 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 90 " -1.016 9.50e-02 1.11e+02 4.55e-01 1.26e+02 pdb=" NE ARG R 90 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG R 90 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG R 90 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 90 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 372 " -0.620 9.50e-02 1.11e+02 2.83e-01 8.39e+01 pdb=" NE ARG R 372 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG R 372 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG R 372 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG R 372 " -0.053 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1065 2.78 - 3.31: 8731 3.31 - 3.84: 14646 3.84 - 4.37: 17937 4.37 - 4.90: 30660 Nonbonded interactions: 73039 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.248 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.307 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.330 3.040 nonbonded pdb=" N ASP B 291 " pdb=" N PHE B 292 " model vdw 2.333 2.560 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.377 3.040 ... (remaining 73034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.230 Find NCS groups from input model: 0.030 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 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 : 0.014 0.460 9145 Z= 0.868 Angle : 2.058 13.344 12398 Z= 1.398 Chirality : 0.130 0.749 1415 Planarity : 0.027 0.455 1562 Dihedral : 13.118 77.685 3243 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.20 % Allowed : 7.02 % Favored : 89.77 % Cbeta Deviations : 2.69 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1127 helix: 2.64 (0.23), residues: 402 sheet: 1.17 (0.30), residues: 261 loop : -0.39 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.130 0.009 ARG A 205 TYR 0.060 0.009 TYR D 161 PHE 0.150 0.009 PHE R 174 TRP 0.045 0.009 TRP B 99 HIS 0.017 0.006 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01253 / 0.82 ( 9143) covalent geometry : angle 2.05642 / 1.40 (12394) SS BOND : bond 0.39556 / 20.20 ( 2) SS BOND : angle 5.29340 / 2.93 ( 4) hydrogen bonds : bond 0.19042 / 12.70 ( 470) hydrogen bonds : angle 7.35929 / 5.19 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 229 ASP cc_start: 0.8570 (m-30) cc_final: 0.8326 (p0) REVERT: A 305 CYS cc_start: 0.9304 (m) cc_final: 0.8719 (m) REVERT: A 333 GLN cc_start: 0.9171 (tp40) cc_final: 0.8790 (tp40) REVERT: B 15 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8667 (mtmm) REVERT: B 197 ARG cc_start: 0.9080 (mmm160) cc_final: 0.8868 (mmm-85) REVERT: R 70 TYR cc_start: 0.8381 (m-10) cc_final: 0.8140 (m-80) REVERT: R 102 HIS cc_start: 0.8988 (m-70) cc_final: 0.8646 (m-70) REVERT: R 103 TYR cc_start: 0.9216 (m-80) cc_final: 0.8704 (m-80) REVERT: R 187 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8532 (tmtt) REVERT: R 205 PHE cc_start: 0.7846 (p90) cc_final: 0.7445 (m-80) REVERT: R 296 GLN cc_start: 0.8974 (tp40) cc_final: 0.8311 (tm-30) REVERT: R 366 LEU cc_start: 0.8205 (tt) cc_final: 0.7891 (mt) REVERT: R 375 PHE cc_start: 0.5106 (OUTLIER) cc_final: 0.4752 (t80) outliers start: 31 outliers final: 6 residues processed: 312 average time/residue: 0.6139 time to fit residues: 202.9045 Evaluate side-chains 194 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 186 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain R residue 375 PHE Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 244 HIS A 294 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN B 6 GLN B 88 ASN B 91 HIS B 259 GLN B 311 HIS C 18 GLN C 59 ASN D 182 ASN R 210 GLN R 229 HIS R 261 ASN R 300 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.062656 restraints weight = 18503.700| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.13 r_work: 0.2933 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9145 Z= 0.170 Angle : 0.670 11.224 12398 Z= 0.355 Chirality : 0.044 0.180 1415 Planarity : 0.005 0.052 1562 Dihedral : 5.765 53.022 1262 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.93 % Allowed : 16.94 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1127 helix: 2.52 (0.25), residues: 403 sheet: 0.84 (0.30), residues: 282 loop : -0.41 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 182 TYR 0.023 0.002 TYR A 230 PHE 0.046 0.002 PHE A 336 TRP 0.022 0.002 TRP B 339 HIS 0.012 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 9143) covalent geometry : angle 0.66766 / 0.35 (12394) SS BOND : bond 0.00706 / 0.36 ( 2) SS BOND : angle 3.34974 / 1.60 ( 4) hydrogen bonds : bond 0.05357 / 3.55 ( 470) hydrogen bonds : angle 5.17252 / 3.64 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.369 Fit side-chains REVERT: A 9 ASP cc_start: 0.8799 (m-30) cc_final: 0.8584 (m-30) REVERT: A 52 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: A 269 ASN cc_start: 0.9284 (m110) cc_final: 0.9073 (m-40) REVERT: A 305 CYS cc_start: 0.8840 (m) cc_final: 0.8496 (m) REVERT: A 306 GLN cc_start: 0.9281 (mm-40) cc_final: 0.9064 (mm-40) REVERT: B 8 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8166 (mtt-85) REVERT: B 15 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8809 (mtmm) REVERT: B 247 ASP cc_start: 0.8139 (m-30) cc_final: 0.7930 (m-30) REVERT: R 102 HIS cc_start: 0.8415 (m-70) cc_final: 0.7951 (m-70) REVERT: R 103 TYR cc_start: 0.9068 (m-80) cc_final: 0.8336 (m-80) REVERT: R 184 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8394 (ttp-170) REVERT: R 187 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8445 (tttt) outliers start: 38 outliers final: 11 residues processed: 211 average time/residue: 0.5837 time to fit residues: 130.5545 Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 373 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 39 GLN D 159 ASN R 81 ASN R 229 HIS R 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060284 restraints weight = 18160.005| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.09 r_work: 0.2860 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9145 Z= 0.158 Angle : 0.624 8.966 12398 Z= 0.330 Chirality : 0.043 0.194 1415 Planarity : 0.004 0.042 1562 Dihedral : 5.138 52.028 1252 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.62 % Allowed : 18.39 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.25), residues: 1127 helix: 2.55 (0.25), residues: 403 sheet: 1.06 (0.30), residues: 287 loop : -0.43 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 268 TYR 0.018 0.002 TYR A 230 PHE 0.016 0.002 PHE R 375 TRP 0.013 0.001 TRP B 339 HIS 0.007 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9143) covalent geometry : angle 0.62197 / 0.33 (12394) SS BOND : bond 0.02010 / 1.05 ( 2) SS BOND : angle 3.17616 / 1.53 ( 4) hydrogen bonds : bond 0.04731 / 3.11 ( 470) hydrogen bonds : angle 4.91580 / 3.44 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.357 Fit side-chains REVERT: A 305 CYS cc_start: 0.8864 (m) cc_final: 0.8550 (m) REVERT: B 8 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8174 (mtt-85) REVERT: B 15 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8811 (mtmm) REVERT: R 102 HIS cc_start: 0.8490 (m-70) cc_final: 0.8177 (m-70) REVERT: R 187 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8422 (tttt) REVERT: R 300 HIS cc_start: 0.8198 (t-90) cc_final: 0.7764 (t-90) REVERT: R 306 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8426 (mtp85) outliers start: 35 outliers final: 13 residues processed: 193 average time/residue: 0.5794 time to fit residues: 118.6450 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 306 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0060 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.0050 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN C 24 ASN D 159 ASN R 229 HIS R 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.058892 restraints weight = 18429.289| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.10 r_work: 0.2826 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9145 Z= 0.156 Angle : 0.594 8.045 12398 Z= 0.309 Chirality : 0.043 0.188 1415 Planarity : 0.004 0.042 1562 Dihedral : 4.976 50.988 1250 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.82 % Allowed : 18.60 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1127 helix: 2.47 (0.26), residues: 411 sheet: 0.95 (0.30), residues: 285 loop : -0.42 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 148 TYR 0.018 0.002 TYR R 145 PHE 0.014 0.001 PHE B 253 TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9143) covalent geometry : angle 0.59197 / 0.31 (12394) SS BOND : bond 0.01640 / 0.86 ( 2) SS BOND : angle 2.67003 / 1.27 ( 4) hydrogen bonds : bond 0.04491 / 2.96 ( 470) hydrogen bonds : angle 4.79121 / 3.35 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.369 Fit side-chains REVERT: A 53 MET cc_start: 0.8198 (tpp) cc_final: 0.7988 (mpp) REVERT: A 305 CYS cc_start: 0.8868 (m) cc_final: 0.8539 (m) REVERT: B 8 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8190 (mpt-90) REVERT: B 15 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8768 (mtmm) REVERT: B 198 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8992 (pp) REVERT: B 291 ASP cc_start: 0.8365 (t0) cc_final: 0.7944 (t0) REVERT: R 102 HIS cc_start: 0.8484 (m-70) cc_final: 0.8207 (m-70) REVERT: R 103 TYR cc_start: 0.9012 (m-80) cc_final: 0.8156 (m-80) REVERT: R 184 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8405 (ttp-170) REVERT: R 300 HIS cc_start: 0.8081 (t-90) cc_final: 0.7660 (t-90) REVERT: R 306 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8367 (mtp85) REVERT: R 328 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7571 (m-10) outliers start: 37 outliers final: 18 residues processed: 182 average time/residue: 0.6519 time to fit residues: 125.4343 Evaluate side-chains 174 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 306 ARG Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 373 HIS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.0010 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN B 268 ASN D 130 GLN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.060458 restraints weight = 18110.232| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.07 r_work: 0.2863 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9145 Z= 0.113 Angle : 0.554 7.883 12398 Z= 0.286 Chirality : 0.041 0.195 1415 Planarity : 0.003 0.039 1562 Dihedral : 4.789 50.130 1250 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.41 % Allowed : 19.63 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1127 helix: 2.57 (0.26), residues: 409 sheet: 0.97 (0.30), residues: 275 loop : -0.44 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 148 TYR 0.015 0.001 TYR R 339 PHE 0.013 0.001 PHE B 253 TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9143) covalent geometry : angle 0.55292 / 0.29 (12394) SS BOND : bond 0.00923 / 0.48 ( 2) SS BOND : angle 1.54531 / 0.74 ( 4) hydrogen bonds : bond 0.03982 / 2.63 ( 470) hydrogen bonds : angle 4.58418 / 3.19 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.382 Fit side-chains REVERT: A 305 CYS cc_start: 0.8868 (m) cc_final: 0.8518 (m) REVERT: B 8 ARG cc_start: 0.8481 (ttm110) cc_final: 0.8222 (mtt90) REVERT: B 15 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8764 (mtmm) REVERT: B 42 ARG cc_start: 0.7792 (ttt-90) cc_final: 0.7555 (ttt-90) REVERT: B 198 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8945 (pp) REVERT: B 252 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9081 (tp) REVERT: B 291 ASP cc_start: 0.8335 (t0) cc_final: 0.7935 (t0) REVERT: B 325 MET cc_start: 0.9323 (mmt) cc_final: 0.8961 (mmt) REVERT: C 58 GLU cc_start: 0.8820 (mp0) cc_final: 0.8602 (pm20) REVERT: R 102 HIS cc_start: 0.8452 (m-70) cc_final: 0.8181 (m-70) REVERT: R 300 HIS cc_start: 0.7914 (t-90) cc_final: 0.7602 (t-90) REVERT: R 328 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7336 (m-10) outliers start: 33 outliers final: 15 residues processed: 182 average time/residue: 0.5561 time to fit residues: 107.5434 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 373 HIS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 255 ASN B 88 ASN B 259 GLN C 24 ASN R 57 ASN R 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.054714 restraints weight = 18208.850| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.10 r_work: 0.2726 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9227 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 9145 Z= 0.285 Angle : 0.672 10.597 12398 Z= 0.353 Chirality : 0.046 0.184 1415 Planarity : 0.004 0.044 1562 Dihedral : 5.337 53.741 1250 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.75 % Allowed : 19.11 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1127 helix: 2.28 (0.25), residues: 422 sheet: 0.81 (0.30), residues: 281 loop : -0.55 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 148 TYR 0.031 0.003 TYR R 145 PHE 0.018 0.002 PHE B 180 TRP 0.021 0.002 TRP R 316 HIS 0.010 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 ( 9143) covalent geometry : angle 0.66697 / 0.35 (12394) SS BOND : bond 0.03012 / 1.58 ( 2) SS BOND : angle 4.49536 / 2.18 ( 4) hydrogen bonds : bond 0.05281 / 3.50 ( 470) hydrogen bonds : angle 4.95631 / 3.47 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.377 Fit side-chains REVERT: A 29 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8681 (ttmm) REVERT: A 305 CYS cc_start: 0.8957 (m) cc_final: 0.8572 (m) REVERT: B 4 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7660 (pt) REVERT: B 8 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8250 (mtt90) REVERT: B 12 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8332 (tm-30) REVERT: B 15 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8788 (mtmm) REVERT: B 172 GLU cc_start: 0.8797 (tp30) cc_final: 0.8550 (tp30) REVERT: B 198 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8993 (pp) REVERT: B 291 ASP cc_start: 0.8459 (t0) cc_final: 0.8046 (t0) REVERT: D 138 THR cc_start: 0.9283 (m) cc_final: 0.9060 (p) REVERT: R 102 HIS cc_start: 0.8542 (m-70) cc_final: 0.8264 (m-70) REVERT: R 103 TYR cc_start: 0.9098 (m-80) cc_final: 0.8207 (m-80) REVERT: R 300 HIS cc_start: 0.8207 (t-90) cc_final: 0.7848 (t-90) REVERT: R 306 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8321 (mtp85) outliers start: 46 outliers final: 16 residues processed: 187 average time/residue: 0.5928 time to fit residues: 117.5038 Evaluate side-chains 172 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain R residue 57 ASN Chi-restraints excluded: chain R residue 306 ARG Chi-restraints excluded: chain R residue 373 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 98 optimal weight: 0.0040 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 36 ASN B 259 GLN C 24 ASN R 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057494 restraints weight = 18441.954| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.12 r_work: 0.2789 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9145 Z= 0.123 Angle : 0.581 10.158 12398 Z= 0.302 Chirality : 0.042 0.192 1415 Planarity : 0.004 0.047 1562 Dihedral : 5.008 55.458 1250 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.10 % Allowed : 21.38 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1127 helix: 2.43 (0.25), residues: 415 sheet: 0.82 (0.30), residues: 275 loop : -0.53 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 148 TYR 0.018 0.001 TYR R 145 PHE 0.010 0.001 PHE B 253 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9143) covalent geometry : angle 0.57994 / 0.30 (12394) SS BOND : bond 0.01091 / 0.57 ( 2) SS BOND : angle 2.32052 / 1.09 ( 4) hydrogen bonds : bond 0.04243 / 2.78 ( 470) hydrogen bonds : angle 4.70675 / 3.28 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.352 Fit side-chains REVERT: A 305 CYS cc_start: 0.8911 (m) cc_final: 0.8524 (m) REVERT: B 4 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7533 (pt) REVERT: B 8 ARG cc_start: 0.8470 (ttm110) cc_final: 0.8186 (mtt90) REVERT: B 12 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8410 (tm-30) REVERT: B 15 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8773 (mtmm) REVERT: B 172 GLU cc_start: 0.8817 (tp30) cc_final: 0.8553 (tp30) REVERT: B 198 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8885 (pp) REVERT: B 252 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9189 (tp) REVERT: B 325 MET cc_start: 0.9360 (mmt) cc_final: 0.9001 (mmt) REVERT: D 138 THR cc_start: 0.9259 (m) cc_final: 0.9021 (p) REVERT: R 102 HIS cc_start: 0.8507 (m-70) cc_final: 0.8217 (m-70) REVERT: R 103 TYR cc_start: 0.9022 (m-80) cc_final: 0.8079 (m-80) REVERT: R 184 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8348 (ttp-170) REVERT: R 187 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8295 (mtmm) REVERT: R 300 HIS cc_start: 0.7967 (t-90) cc_final: 0.7681 (t-90) REVERT: R 306 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8210 (mtp85) outliers start: 30 outliers final: 15 residues processed: 180 average time/residue: 0.6514 time to fit residues: 123.9591 Evaluate side-chains 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 306 ARG Chi-restraints excluded: chain R residue 373 HIS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 77 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 269 ASN A 346 ASN B 36 ASN ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057988 restraints weight = 18171.656| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.07 r_work: 0.2800 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9145 Z= 0.130 Angle : 0.582 9.423 12398 Z= 0.299 Chirality : 0.041 0.205 1415 Planarity : 0.004 0.053 1562 Dihedral : 4.904 55.940 1250 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.10 % Allowed : 22.00 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1127 helix: 2.50 (0.25), residues: 415 sheet: 0.79 (0.30), residues: 276 loop : -0.52 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 148 TYR 0.016 0.001 TYR R 339 PHE 0.010 0.001 PHE B 253 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9143) covalent geometry : angle 0.58110 / 0.30 (12394) SS BOND : bond 0.01310 / 0.68 ( 2) SS BOND : angle 2.29571 / 1.08 ( 4) hydrogen bonds : bond 0.04091 / 2.69 ( 470) hydrogen bonds : angle 4.63995 / 3.22 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8499 (ttmm) REVERT: A 296 TYR cc_start: 0.8781 (t80) cc_final: 0.7682 (t80) REVERT: A 305 CYS cc_start: 0.8919 (m) cc_final: 0.8508 (m) REVERT: B 12 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8312 (tm-30) REVERT: B 15 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: B 172 GLU cc_start: 0.8779 (tp30) cc_final: 0.8505 (tp30) REVERT: B 198 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8870 (pp) REVERT: B 252 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9175 (tp) REVERT: B 291 ASP cc_start: 0.8372 (t0) cc_final: 0.7925 (t0) REVERT: B 325 MET cc_start: 0.9355 (mmt) cc_final: 0.8974 (mmt) REVERT: D 138 THR cc_start: 0.9249 (m) cc_final: 0.8949 (p) REVERT: R 102 HIS cc_start: 0.8527 (m-70) cc_final: 0.8230 (m-70) REVERT: R 103 TYR cc_start: 0.8997 (m-80) cc_final: 0.8572 (m-80) REVERT: R 184 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8314 (ttp-170) REVERT: R 187 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8249 (mtmm) REVERT: R 300 HIS cc_start: 0.7864 (t-90) cc_final: 0.7601 (t-90) REVERT: R 306 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8161 (mtp85) outliers start: 30 outliers final: 14 residues processed: 184 average time/residue: 0.5752 time to fit residues: 112.0131 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 306 ARG Chi-restraints excluded: chain R residue 373 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 346 ASN B 36 ASN ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056362 restraints weight = 18564.996| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.13 r_work: 0.2769 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9145 Z= 0.182 Angle : 0.625 10.185 12398 Z= 0.320 Chirality : 0.043 0.197 1415 Planarity : 0.004 0.058 1562 Dihedral : 4.996 57.009 1250 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.31 % Allowed : 22.00 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1127 helix: 2.49 (0.25), residues: 415 sheet: 0.68 (0.30), residues: 283 loop : -0.57 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 148 TYR 0.016 0.002 TYR R 339 PHE 0.015 0.001 PHE A 336 TRP 0.015 0.001 TRP R 316 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 9143) covalent geometry : angle 0.62252 / 0.32 (12394) SS BOND : bond 0.01785 / 0.93 ( 2) SS BOND : angle 2.88699 / 1.37 ( 4) hydrogen bonds : bond 0.04403 / 2.91 ( 470) hydrogen bonds : angle 4.72975 / 3.29 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8578 (ttmm) REVERT: A 52 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: A 305 CYS cc_start: 0.8960 (m) cc_final: 0.8529 (m) REVERT: B 6 GLN cc_start: 0.8873 (pp30) cc_final: 0.8643 (pp30) REVERT: B 8 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8162 (mtt90) REVERT: B 12 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8319 (tm-30) REVERT: B 15 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8762 (mtmm) REVERT: B 172 GLU cc_start: 0.8822 (tp30) cc_final: 0.8568 (tp30) REVERT: B 198 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8916 (pp) REVERT: B 252 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9195 (tp) REVERT: B 291 ASP cc_start: 0.8435 (t0) cc_final: 0.8028 (t0) REVERT: B 325 MET cc_start: 0.9377 (mmt) cc_final: 0.9007 (mmt) REVERT: R 84 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.9027 (m) REVERT: R 103 TYR cc_start: 0.9038 (m-80) cc_final: 0.8270 (m-80) REVERT: R 184 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8340 (ttp-170) REVERT: R 187 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8276 (mtmm) REVERT: R 300 HIS cc_start: 0.7937 (t-90) cc_final: 0.7672 (t-90) REVERT: R 306 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8205 (mtp85) outliers start: 32 outliers final: 13 residues processed: 178 average time/residue: 0.7204 time to fit residues: 135.1347 Evaluate side-chains 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 306 ARG Chi-restraints excluded: chain R residue 373 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 269 ASN B 36 ASN D 130 GLN ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN R 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055961 restraints weight = 18605.052| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.14 r_work: 0.2760 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9145 Z= 0.184 Angle : 0.643 10.596 12398 Z= 0.325 Chirality : 0.043 0.201 1415 Planarity : 0.004 0.061 1562 Dihedral : 5.054 58.095 1250 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.79 % Allowed : 22.21 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.25), residues: 1127 helix: 2.55 (0.25), residues: 415 sheet: 0.70 (0.30), residues: 276 loop : -0.64 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 148 TYR 0.018 0.002 TYR R 145 PHE 0.012 0.001 PHE R 127 TRP 0.015 0.001 TRP R 316 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 9143) covalent geometry : angle 0.64091 / 0.32 (12394) SS BOND : bond 0.01790 / 0.94 ( 2) SS BOND : angle 2.87835 / 1.36 ( 4) hydrogen bonds : bond 0.04468 / 2.95 ( 470) hydrogen bonds : angle 4.74714 / 3.29 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8605 (ttmm) REVERT: A 52 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: A 305 CYS cc_start: 0.8911 (m) cc_final: 0.8482 (m) REVERT: B 6 GLN cc_start: 0.8881 (pp30) cc_final: 0.8651 (pp30) REVERT: B 8 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8181 (mtt90) REVERT: B 12 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8364 (tm-30) REVERT: B 15 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8778 (mtmm) REVERT: B 172 GLU cc_start: 0.8840 (tp30) cc_final: 0.8589 (tp30) REVERT: B 198 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8910 (pp) REVERT: B 252 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9176 (tp) REVERT: B 291 ASP cc_start: 0.8437 (t0) cc_final: 0.8006 (t0) REVERT: B 325 MET cc_start: 0.9383 (mmt) cc_final: 0.9010 (mmt) REVERT: R 84 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9041 (m) REVERT: R 103 TYR cc_start: 0.9049 (m-80) cc_final: 0.8314 (m-80) REVERT: R 184 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8329 (ttp-170) REVERT: R 187 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8298 (mtmm) REVERT: R 306 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8236 (mtp85) outliers start: 27 outliers final: 15 residues processed: 170 average time/residue: 0.6964 time to fit residues: 124.8831 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 306 ARG Chi-restraints excluded: chain R residue 373 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 36 ASN ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057066 restraints weight = 18350.591| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.12 r_work: 0.2788 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9145 Z= 0.141 Angle : 0.611 10.264 12398 Z= 0.310 Chirality : 0.042 0.204 1415 Planarity : 0.004 0.061 1562 Dihedral : 4.927 57.900 1250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.48 % Allowed : 22.93 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1127 helix: 2.59 (0.25), residues: 415 sheet: 0.67 (0.31), residues: 272 loop : -0.63 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 148 TYR 0.015 0.001 TYR R 339 PHE 0.018 0.001 PHE A 336 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9143) covalent geometry : angle 0.60939 / 0.31 (12394) SS BOND : bond 0.01306 / 0.68 ( 2) SS BOND : angle 2.28637 / 1.08 ( 4) hydrogen bonds : bond 0.04151 / 2.73 ( 470) hydrogen bonds : angle 4.66321 / 3.23 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.87 seconds wall clock time: 70 minutes 27.35 seconds (4227.35 seconds total)