Starting phenix.real_space_refine on Sun Aug 24 06:57:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibv_35346/08_2025/8ibv_35346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibv_35346/08_2025/8ibv_35346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibv_35346/08_2025/8ibv_35346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibv_35346/08_2025/8ibv_35346.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibv_35346/08_2025/8ibv_35346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibv_35346/08_2025/8ibv_35346.cif" } resolution = 3.19 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= 0.029 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5759 2.51 5 N 1569 2.21 5 O 1672 1.98 5 H 9023 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 18081 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4539 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 3 Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 332 Classifications: {'peptide': 19} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "A" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3815 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 5089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5089 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3479 Classifications: {'peptide': 230} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 827 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Time building chain proxies: 3.64, per 1000 atoms: 0.20 Number of scatterers: 18081 At special positions: 0 Unit cell: (123.6, 91.464, 137.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 O 1672 8.00 N 1569 7.00 C 5759 6.00 H 9023 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 235 " distance=2.02 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: 1.67 Conformation dependent library (CDL) restraints added in 657.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 38.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'R' and resid 34 through 66 removed outlier: 3.898A pdb=" N VAL R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) Proline residue: R 40 - end of helix removed outlier: 3.632A pdb=" N TYR R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 89 Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 107 through 141 removed outlier: 3.645A pdb=" N GLY R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 170 Processing helix chain 'R' and resid 171 through 175 Processing helix chain 'R' and resid 226 through 231 Processing helix chain 'R' and resid 241 through 253 removed outlier: 3.580A pdb=" N THR R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 275 removed outlier: 3.554A pdb=" N LEU R 258 " --> pdb=" O ALA R 254 " (cutoff:3.500A) Proline residue: R 259 - end of helix Processing helix chain 'R' and resid 293 through 322 Proline residue: R 313 - end of helix Processing helix chain 'R' and resid 326 through 356 removed outlier: 3.693A pdb=" N TYR R 335 " --> pdb=" O TYR R 331 " (cutoff:3.500A) Proline residue: R 352 - end of helix Processing helix chain 'R' and resid 359 through 371 Processing helix chain 'C' and resid 6 through 18 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.612A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.531A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.547A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.640A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.715A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.579A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.849A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.989A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.901A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.860A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 3.599A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.666A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 76 " --> pdb=" O HIS B 67 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.535A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 127 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.767A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 194 removed outlier: 7.373A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 208 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.877A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.769A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.748A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 91 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 116 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.728A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8993 1.02 - 1.22: 38 1.22 - 1.41: 3822 1.41 - 1.61: 5327 1.61 - 1.81: 85 Bond restraints: 18265 Sorted by residual: bond pdb=" CA GLU R 226 " pdb=" C GLU R 226 " ideal model delta sigma weight residual 1.524 1.668 -0.144 1.32e-02 5.74e+03 1.19e+02 bond pdb=" SG CYS R 30 " pdb=" HG CYS R 30 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" N ARG R 236 " pdb=" CA ARG R 236 " ideal model delta sigma weight residual 1.455 1.389 0.066 9.60e-03 1.09e+04 4.72e+01 bond pdb=" CA ARG R 236 " pdb=" C ARG R 236 " ideal model delta sigma weight residual 1.519 1.446 0.073 1.09e-02 8.42e+03 4.43e+01 bond pdb=" C ALA R 227 " pdb=" O ALA R 227 " ideal model delta sigma weight residual 1.236 1.315 -0.080 1.32e-02 5.74e+03 3.63e+01 ... (remaining 18260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 32647 2.37 - 4.73: 190 4.73 - 7.10: 25 7.10 - 9.47: 2 9.47 - 11.83: 6 Bond angle restraints: 32870 Sorted by residual: angle pdb=" N ALA R 228 " pdb=" CA ALA R 228 " pdb=" C ALA R 228 " ideal model delta sigma weight residual 111.14 99.31 11.83 1.08e+00 8.57e-01 1.20e+02 angle pdb=" N ARG R 236 " pdb=" CA ARG R 236 " pdb=" C ARG R 236 " ideal model delta sigma weight residual 108.25 97.25 11.00 1.16e+00 7.43e-01 8.99e+01 angle pdb=" N GLU R 180 " pdb=" CA GLU R 180 " pdb=" C GLU R 180 " ideal model delta sigma weight residual 110.35 99.00 11.35 1.36e+00 5.41e-01 6.96e+01 angle pdb=" N GLN R 181 " pdb=" CA GLN R 181 " pdb=" C GLN R 181 " ideal model delta sigma weight residual 112.94 124.39 -11.45 1.41e+00 5.03e-01 6.60e+01 angle pdb=" N LEU R 230 " pdb=" CA LEU R 230 " pdb=" C LEU R 230 " ideal model delta sigma weight residual 112.34 122.44 -10.10 1.30e+00 5.92e-01 6.04e+01 ... (remaining 32865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8259 17.66 - 35.33: 198 35.33 - 52.99: 97 52.99 - 70.65: 38 70.65 - 88.31: 7 Dihedral angle restraints: 8599 sinusoidal: 4636 harmonic: 3963 Sorted by residual: dihedral pdb=" CD ARG R 233 " pdb=" NE ARG R 233 " pdb=" CZ ARG R 233 " pdb=" NH1 ARG R 233 " ideal model delta sinusoidal sigma weight residual 0.00 -79.73 79.73 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 235 " pdb=" CB CYS R 235 " ideal model delta sinusoidal sigma weight residual 93.00 149.37 -56.37 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CA ASP R 94 " pdb=" CB ASP R 94 " pdb=" CG ASP R 94 " pdb=" OD1 ASP R 94 " ideal model delta sinusoidal sigma weight residual -30.00 -86.74 56.74 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 8596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1337 0.098 - 0.196: 73 0.196 - 0.295: 5 0.295 - 0.393: 1 0.393 - 0.491: 1 Chirality restraints: 1417 Sorted by residual: chirality pdb=" CA GLN R 181 " pdb=" N GLN R 181 " pdb=" C GLN R 181 " pdb=" CB GLN R 181 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA LEU R 230 " pdb=" N LEU R 230 " pdb=" C LEU R 230 " pdb=" CB LEU R 230 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA GLU R 226 " pdb=" N GLU R 226 " pdb=" C GLU R 226 " pdb=" CB GLU R 226 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1414 not shown) Planarity restraints: 2690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 181 " -0.099 2.00e-02 2.50e+03 4.24e-01 2.70e+03 pdb=" CD GLN R 181 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN R 181 " 0.092 2.00e-02 2.50e+03 pdb=" NE2 GLN R 181 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN R 181 " 0.722 2.00e-02 2.50e+03 pdb="HE22 GLN R 181 " -0.735 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 233 " 1.299 9.50e-02 1.11e+02 4.75e-01 1.04e+03 pdb=" NE ARG R 233 " 0.093 2.00e-02 2.50e+03 pdb=" CZ ARG R 233 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG R 233 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG R 233 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG R 233 " -0.095 2.00e-02 2.50e+03 pdb="HH12 ARG R 233 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG R 233 " -0.399 2.00e-02 2.50e+03 pdb="HH22 ARG R 233 " 0.401 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 179 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C VAL R 179 " -0.082 2.00e-02 2.50e+03 pdb=" O VAL R 179 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU R 180 " 0.027 2.00e-02 2.50e+03 ... (remaining 2687 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 231 2.06 - 2.70: 28692 2.70 - 3.33: 51257 3.33 - 3.97: 65592 3.97 - 4.60: 102705 Nonbonded interactions: 248477 Sorted by model distance: nonbonded pdb=" HE ARG R 236 " pdb=" HG1 THR C 6 " model vdw 1.426 2.100 nonbonded pdb=" OD1 ASP B 158 " pdb=" H GLN B 161 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASN A 259 " pdb=" H LYS A 260 " model vdw 1.666 2.450 nonbonded pdb=" O SER R 333 " pdb="HD21 ASN R 337 " model vdw 1.667 2.450 nonbonded pdb="HH21 ARG A 205 " pdb=" OD1 ASP B 191 " model vdw 1.674 2.450 ... (remaining 248472 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: 1.100 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: 0.110 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 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 : 0.004 0.144 9243 Z= 0.289 Angle : 0.549 11.834 12520 Z= 0.364 Chirality : 0.045 0.491 1417 Planarity : 0.012 0.476 1588 Dihedral : 7.468 88.314 3345 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.97 % 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: -0.45 (0.24), residues: 1128 helix: 1.15 (0.25), residues: 399 sheet: -0.39 (0.31), residues: 236 loop : -1.47 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 233 TYR 0.009 0.000 TYR R 96 PHE 0.013 0.001 PHE R 231 TRP 0.002 0.000 TRP E 110 HIS 0.001 0.000 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9242) covalent geometry : angle 0.54811 (12518) SS BOND : bond 0.01577 ( 1) SS BOND : angle 3.08137 ( 2) hydrogen bonds : bond 0.19133 ( 442) hydrogen bonds : angle 6.68340 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 355 TYR cc_start: 0.6289 (m-80) cc_final: 0.4864 (m-80) REVERT: A 188 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7448 (ttpp) REVERT: A 242 SER cc_start: 0.8250 (t) cc_final: 0.7973 (p) REVERT: A 247 ARG cc_start: 0.6835 (ttm170) cc_final: 0.6585 (ttm170) REVERT: A 275 ILE cc_start: 0.8025 (mt) cc_final: 0.7616 (mt) REVERT: A 314 ASP cc_start: 0.6960 (t0) cc_final: 0.6759 (t0) REVERT: B 63 ILE cc_start: 0.7925 (mt) cc_final: 0.7674 (mt) REVERT: B 168 ASP cc_start: 0.7647 (p0) cc_final: 0.7247 (p0) REVERT: B 180 GLN cc_start: 0.6601 (mm-40) cc_final: 0.6260 (mm-40) REVERT: B 300 ASN cc_start: 0.7988 (m-40) cc_final: 0.7766 (m110) REVERT: E 42 LYS cc_start: 0.8024 (tptt) cc_final: 0.7788 (tptt) REVERT: E 88 GLU cc_start: 0.5997 (mp0) cc_final: 0.5743 (mp0) REVERT: E 115 THR cc_start: 0.8340 (t) cc_final: 0.8047 (p) REVERT: G 28 LYS cc_start: 0.7376 (mtmt) cc_final: 0.7045 (mtmt) REVERT: G 45 LYS cc_start: 0.7695 (mmtm) cc_final: 0.7309 (mmtm) outliers start: 1 outliers final: 1 residues processed: 255 average time/residue: 0.2839 time to fit residues: 94.3634 Evaluate side-chains 229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS B 161 GLN B 225 GLN B 235 ASN E 76 ASN E 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123718 restraints weight = 34726.092| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.90 r_work: 0.3392 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9243 Z= 0.295 Angle : 0.633 8.216 12520 Z= 0.335 Chirality : 0.045 0.240 1417 Planarity : 0.005 0.048 1588 Dihedral : 4.265 52.571 1265 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.73 % Allowed : 7.43 % Favored : 90.84 % 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: -0.02 (0.24), residues: 1128 helix: 1.23 (0.25), residues: 416 sheet: -0.46 (0.30), residues: 274 loop : -0.84 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 256 TYR 0.037 0.002 TYR E 190 PHE 0.027 0.003 PHE R 314 TRP 0.014 0.002 TRP B 87 HIS 0.010 0.002 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 9242) covalent geometry : angle 0.63276 (12518) SS BOND : bond 0.00064 ( 1) SS BOND : angle 1.07907 ( 2) hydrogen bonds : bond 0.04694 ( 442) hydrogen bonds : angle 4.68239 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: A 188 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7701 (ttpp) REVERT: A 208 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7381 (ttm110) REVERT: A 239 ASP cc_start: 0.7344 (t0) cc_final: 0.7107 (t0) REVERT: A 241 LYS cc_start: 0.8106 (tttp) cc_final: 0.7826 (ttmm) REVERT: A 247 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7613 (ttm170) REVERT: A 257 PHE cc_start: 0.8356 (m-10) cc_final: 0.7927 (m-80) REVERT: A 258 LEU cc_start: 0.7887 (mt) cc_final: 0.7628 (mp) REVERT: A 281 GLU cc_start: 0.6995 (tp30) cc_final: 0.6777 (tp30) REVERT: A 314 ASP cc_start: 0.7570 (t0) cc_final: 0.7195 (t0) REVERT: A 347 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7909 (ttpp) REVERT: B 47 ARG cc_start: 0.6127 (mtm-85) cc_final: 0.5904 (mtm-85) REVERT: B 273 ASN cc_start: 0.7260 (t0) cc_final: 0.6927 (t0) REVERT: B 339 SER cc_start: 0.7860 (m) cc_final: 0.7411 (t) REVERT: E 86 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7408 (mtt180) REVERT: E 88 GLU cc_start: 0.7018 (mp0) cc_final: 0.6666 (mp0) REVERT: E 213 THR cc_start: 0.7880 (m) cc_final: 0.7539 (p) REVERT: E 215 THR cc_start: 0.7783 (m) cc_final: 0.7449 (p) REVERT: G 20 MET cc_start: 0.7030 (mmm) cc_final: 0.6668 (mmm) REVERT: G 45 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7600 (mmtm) outliers start: 17 outliers final: 14 residues processed: 260 average time/residue: 0.2896 time to fit residues: 98.3875 Evaluate side-chains 252 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 356 ASN A 324 HIS B 244 ASN B 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123649 restraints weight = 35297.946| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.86 r_work: 0.3400 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9243 Z= 0.131 Angle : 0.462 5.525 12520 Z= 0.244 Chirality : 0.039 0.165 1417 Planarity : 0.004 0.045 1588 Dihedral : 3.917 52.181 1265 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.93 % Allowed : 10.07 % Favored : 88.00 % 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: 0.63 (0.25), residues: 1128 helix: 2.01 (0.25), residues: 414 sheet: -0.39 (0.30), residues: 287 loop : -0.51 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 236 TYR 0.021 0.001 TYR E 190 PHE 0.013 0.001 PHE R 314 TRP 0.013 0.001 TRP A 244 HIS 0.017 0.002 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9242) covalent geometry : angle 0.46177 (12518) SS BOND : bond 0.00277 ( 1) SS BOND : angle 0.61623 ( 2) hydrogen bonds : bond 0.03756 ( 442) hydrogen bonds : angle 4.25791 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8001 (ttpp) cc_final: 0.7682 (ttpp) REVERT: A 247 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7534 (ttm170) REVERT: A 258 LEU cc_start: 0.7881 (mt) cc_final: 0.7549 (mp) REVERT: A 281 GLU cc_start: 0.7002 (tp30) cc_final: 0.6792 (tp30) REVERT: A 314 ASP cc_start: 0.7597 (t0) cc_final: 0.7251 (t0) REVERT: A 331 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7580 (p) REVERT: B 160 ASN cc_start: 0.8136 (t0) cc_final: 0.7924 (t0) REVERT: B 273 ASN cc_start: 0.7240 (t0) cc_final: 0.6905 (t0) REVERT: B 339 SER cc_start: 0.7820 (m) cc_final: 0.7332 (t) REVERT: E 86 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7436 (mtt180) REVERT: E 88 GLU cc_start: 0.7125 (mp0) cc_final: 0.6755 (mp0) REVERT: E 213 THR cc_start: 0.7958 (m) cc_final: 0.7563 (p) REVERT: G 20 MET cc_start: 0.6912 (mmm) cc_final: 0.6550 (mmm) REVERT: G 45 LYS cc_start: 0.7980 (mmtm) cc_final: 0.7620 (mmtm) outliers start: 19 outliers final: 12 residues processed: 240 average time/residue: 0.2952 time to fit residues: 91.6884 Evaluate side-chains 238 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 254 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 0.0010 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.141469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119959 restraints weight = 35323.568| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.86 r_work: 0.3354 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9243 Z= 0.174 Angle : 0.484 5.886 12520 Z= 0.255 Chirality : 0.040 0.167 1417 Planarity : 0.004 0.050 1588 Dihedral : 3.736 17.635 1263 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.32 % Allowed : 10.48 % Favored : 88.20 % 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 (0.25), residues: 1128 helix: 2.17 (0.26), residues: 411 sheet: -0.28 (0.30), residues: 278 loop : -0.44 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 323 TYR 0.028 0.001 TYR E 190 PHE 0.014 0.001 PHE R 314 TRP 0.012 0.001 TRP B 216 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9242) covalent geometry : angle 0.48368 (12518) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.52863 ( 2) hydrogen bonds : bond 0.03798 ( 442) hydrogen bonds : angle 4.18291 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7723 (ttpp) REVERT: A 247 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7554 (ttm170) REVERT: A 281 GLU cc_start: 0.6997 (tp30) cc_final: 0.6778 (tp30) REVERT: A 314 ASP cc_start: 0.7633 (t0) cc_final: 0.7326 (t0) REVERT: B 84 LEU cc_start: 0.8339 (mt) cc_final: 0.8093 (mp) REVERT: B 151 LEU cc_start: 0.7615 (mt) cc_final: 0.7405 (mt) REVERT: B 273 ASN cc_start: 0.7259 (t0) cc_final: 0.6938 (t0) REVERT: B 339 SER cc_start: 0.7869 (m) cc_final: 0.7407 (t) REVERT: E 86 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7542 (mtt180) REVERT: E 88 GLU cc_start: 0.7192 (mp0) cc_final: 0.6842 (mp0) REVERT: E 213 THR cc_start: 0.8032 (m) cc_final: 0.7655 (p) REVERT: G 20 MET cc_start: 0.6979 (mmm) cc_final: 0.6597 (mmm) REVERT: G 45 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7607 (mmtm) outliers start: 13 outliers final: 10 residues processed: 226 average time/residue: 0.3234 time to fit residues: 93.3874 Evaluate side-chains 224 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 254 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121807 restraints weight = 35018.275| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.86 r_work: 0.3368 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9243 Z= 0.115 Angle : 0.440 5.120 12520 Z= 0.230 Chirality : 0.038 0.157 1417 Planarity : 0.003 0.045 1588 Dihedral : 3.575 18.300 1263 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.73 % Allowed : 11.19 % Favored : 87.08 % 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: 1.09 (0.26), residues: 1128 helix: 2.49 (0.26), residues: 411 sheet: -0.12 (0.31), residues: 271 loop : -0.37 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 97 TYR 0.019 0.001 TYR E 190 PHE 0.011 0.001 PHE R 314 TRP 0.010 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9242) covalent geometry : angle 0.44041 (12518) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.42487 ( 2) hydrogen bonds : bond 0.03371 ( 442) hydrogen bonds : angle 4.00269 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.6720 (tmm) cc_final: 0.6488 (tmm) REVERT: A 188 LYS cc_start: 0.8050 (ttpp) cc_final: 0.7847 (ttpp) REVERT: A 247 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7560 (ttm170) REVERT: A 281 GLU cc_start: 0.6985 (tp30) cc_final: 0.6757 (tp30) REVERT: A 314 ASP cc_start: 0.7599 (t0) cc_final: 0.7298 (t0) REVERT: B 84 LEU cc_start: 0.8317 (mt) cc_final: 0.8096 (mp) REVERT: B 273 ASN cc_start: 0.7260 (t0) cc_final: 0.6930 (t0) REVERT: B 339 SER cc_start: 0.7854 (m) cc_final: 0.7345 (t) REVERT: E 86 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7531 (mtt180) REVERT: E 88 GLU cc_start: 0.7194 (mp0) cc_final: 0.6833 (mp0) REVERT: E 115 THR cc_start: 0.8601 (t) cc_final: 0.8148 (p) REVERT: E 213 THR cc_start: 0.8052 (m) cc_final: 0.7700 (p) REVERT: G 20 MET cc_start: 0.6976 (mmm) cc_final: 0.6598 (mmm) REVERT: G 45 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7608 (mmtm) outliers start: 17 outliers final: 14 residues processed: 226 average time/residue: 0.3060 time to fit residues: 89.0337 Evaluate side-chains 229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 327 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 324 HIS B 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118355 restraints weight = 34512.125| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.82 r_work: 0.3322 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9243 Z= 0.241 Angle : 0.529 6.701 12520 Z= 0.281 Chirality : 0.041 0.197 1417 Planarity : 0.004 0.053 1588 Dihedral : 4.088 18.268 1263 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.73 % Allowed : 11.80 % Favored : 86.47 % 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: 0.88 (0.25), residues: 1128 helix: 2.13 (0.25), residues: 411 sheet: -0.15 (0.32), residues: 272 loop : -0.33 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 97 TYR 0.036 0.002 TYR E 190 PHE 0.018 0.002 PHE R 344 TRP 0.014 0.002 TRP B 216 HIS 0.006 0.002 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 9242) covalent geometry : angle 0.52855 (12518) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.59144 ( 2) hydrogen bonds : bond 0.04262 ( 442) hydrogen bonds : angle 4.32360 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.6382 (tmm) cc_final: 0.6162 (tmm) REVERT: R 314 PHE cc_start: 0.7392 (t80) cc_final: 0.7159 (t80) REVERT: C 9 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 188 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7853 (ttpp) REVERT: A 217 ASP cc_start: 0.6812 (t70) cc_final: 0.6511 (t0) REVERT: A 281 GLU cc_start: 0.6882 (tp30) cc_final: 0.6593 (tp30) REVERT: A 314 ASP cc_start: 0.7467 (t0) cc_final: 0.7147 (t0) REVERT: A 331 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 47 ARG cc_start: 0.6386 (mtm-85) cc_final: 0.6178 (mmm-85) REVERT: B 273 ASN cc_start: 0.7177 (t0) cc_final: 0.6878 (t0) REVERT: B 339 SER cc_start: 0.7986 (m) cc_final: 0.7623 (p) REVERT: E 88 GLU cc_start: 0.7269 (mp0) cc_final: 0.6908 (mp0) REVERT: E 115 THR cc_start: 0.8523 (t) cc_final: 0.8053 (p) REVERT: E 213 THR cc_start: 0.8165 (m) cc_final: 0.7800 (p) REVERT: E 238 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8065 (p) REVERT: G 20 MET cc_start: 0.7139 (mmm) cc_final: 0.6726 (mmm) REVERT: G 45 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7560 (mmtm) outliers start: 17 outliers final: 13 residues processed: 214 average time/residue: 0.3307 time to fit residues: 90.1347 Evaluate side-chains 218 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.139982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118918 restraints weight = 34844.420| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.79 r_work: 0.3322 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9243 Z= 0.181 Angle : 0.488 5.969 12520 Z= 0.259 Chirality : 0.040 0.158 1417 Planarity : 0.004 0.051 1588 Dihedral : 3.987 19.069 1263 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.63 % Allowed : 12.82 % Favored : 85.55 % 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: 0.99 (0.26), residues: 1128 helix: 2.26 (0.25), residues: 415 sheet: -0.16 (0.32), residues: 261 loop : -0.30 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 97 TYR 0.027 0.001 TYR E 190 PHE 0.011 0.001 PHE R 344 TRP 0.012 0.001 TRP A 211 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9242) covalent geometry : angle 0.48801 (12518) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.54715 ( 2) hydrogen bonds : bond 0.03888 ( 442) hydrogen bonds : angle 4.24931 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 314 PHE cc_start: 0.7338 (t80) cc_final: 0.7090 (t80) REVERT: C 9 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6757 (mt-10) REVERT: A 188 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7833 (ttpp) REVERT: A 217 ASP cc_start: 0.6749 (t70) cc_final: 0.6440 (t0) REVERT: A 281 GLU cc_start: 0.6902 (tp30) cc_final: 0.6603 (tp30) REVERT: A 314 ASP cc_start: 0.7519 (t0) cc_final: 0.7209 (t0) REVERT: B 151 LEU cc_start: 0.7586 (mt) cc_final: 0.7360 (mt) REVERT: B 273 ASN cc_start: 0.7163 (t0) cc_final: 0.6863 (t0) REVERT: B 339 SER cc_start: 0.7982 (m) cc_final: 0.7586 (p) REVERT: E 88 GLU cc_start: 0.7277 (mp0) cc_final: 0.6917 (mp0) REVERT: E 160 ARG cc_start: 0.7286 (ttm-80) cc_final: 0.7058 (ttm-80) REVERT: E 213 THR cc_start: 0.8189 (m) cc_final: 0.7816 (p) REVERT: E 215 THR cc_start: 0.8062 (m) cc_final: 0.7571 (p) REVERT: E 238 THR cc_start: 0.8386 (m) cc_final: 0.8074 (p) REVERT: G 20 MET cc_start: 0.7108 (mmm) cc_final: 0.6698 (mmm) REVERT: G 45 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7577 (mmtm) outliers start: 16 outliers final: 14 residues processed: 220 average time/residue: 0.3255 time to fit residues: 91.2942 Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.0010 chunk 103 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118195 restraints weight = 34514.778| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.81 r_work: 0.3312 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9243 Z= 0.207 Angle : 0.501 5.907 12520 Z= 0.265 Chirality : 0.040 0.169 1417 Planarity : 0.004 0.052 1588 Dihedral : 4.059 18.597 1263 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.03 % Allowed : 12.21 % Favored : 85.76 % 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: 0.98 (0.25), residues: 1128 helix: 2.22 (0.25), residues: 415 sheet: -0.11 (0.32), residues: 260 loop : -0.29 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 97 TYR 0.029 0.002 TYR E 190 PHE 0.013 0.001 PHE R 344 TRP 0.012 0.001 TRP B 216 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 9242) covalent geometry : angle 0.50058 (12518) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.58050 ( 2) hydrogen bonds : bond 0.03984 ( 442) hydrogen bonds : angle 4.29308 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 314 PHE cc_start: 0.7342 (t80) cc_final: 0.7107 (t80) REVERT: A 217 ASP cc_start: 0.6813 (t70) cc_final: 0.6483 (t0) REVERT: A 281 GLU cc_start: 0.6903 (tp30) cc_final: 0.6584 (tp30) REVERT: A 314 ASP cc_start: 0.7510 (t0) cc_final: 0.7194 (t0) REVERT: B 273 ASN cc_start: 0.7146 (t0) cc_final: 0.6848 (t0) REVERT: B 339 SER cc_start: 0.7991 (m) cc_final: 0.7585 (p) REVERT: E 88 GLU cc_start: 0.7309 (mp0) cc_final: 0.6947 (mp0) REVERT: E 160 ARG cc_start: 0.7332 (ttm-80) cc_final: 0.7087 (ttm-80) REVERT: E 213 THR cc_start: 0.8228 (m) cc_final: 0.7858 (p) REVERT: E 215 THR cc_start: 0.8090 (m) cc_final: 0.7595 (p) REVERT: E 238 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (p) REVERT: G 20 MET cc_start: 0.7133 (mmm) cc_final: 0.6735 (mmm) REVERT: G 45 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7557 (mmtm) outliers start: 20 outliers final: 15 residues processed: 220 average time/residue: 0.3290 time to fit residues: 91.8414 Evaluate side-chains 228 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 347 SER Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119136 restraints weight = 34469.152| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.83 r_work: 0.3333 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9243 Z= 0.142 Angle : 0.472 5.568 12520 Z= 0.249 Chirality : 0.039 0.158 1417 Planarity : 0.004 0.048 1588 Dihedral : 3.954 18.331 1263 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.53 % Allowed : 13.02 % Favored : 85.45 % 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: 1.09 (0.26), residues: 1128 helix: 2.38 (0.26), residues: 415 sheet: -0.03 (0.33), residues: 253 loop : -0.33 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 97 TYR 0.024 0.001 TYR E 190 PHE 0.011 0.001 PHE E 79 TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9242) covalent geometry : angle 0.47176 (12518) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.45694 ( 2) hydrogen bonds : bond 0.03714 ( 442) hydrogen bonds : angle 4.18274 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 314 PHE cc_start: 0.7296 (t80) cc_final: 0.7044 (t80) REVERT: C 9 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 217 ASP cc_start: 0.6757 (t70) cc_final: 0.6430 (t0) REVERT: A 258 LEU cc_start: 0.7896 (mt) cc_final: 0.7606 (mp) REVERT: A 281 GLU cc_start: 0.6911 (tp30) cc_final: 0.6586 (tp30) REVERT: A 314 ASP cc_start: 0.7542 (t0) cc_final: 0.7226 (t0) REVERT: B 151 LEU cc_start: 0.7587 (mt) cc_final: 0.7361 (mt) REVERT: B 273 ASN cc_start: 0.7151 (t0) cc_final: 0.6840 (t0) REVERT: B 339 SER cc_start: 0.7933 (m) cc_final: 0.7506 (p) REVERT: E 88 GLU cc_start: 0.7300 (mp0) cc_final: 0.6948 (mp0) REVERT: E 160 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.7073 (ttm-80) REVERT: E 213 THR cc_start: 0.8218 (m) cc_final: 0.7846 (p) REVERT: E 215 THR cc_start: 0.8091 (m) cc_final: 0.7627 (p) REVERT: G 20 MET cc_start: 0.7140 (mmm) cc_final: 0.6738 (mmm) REVERT: G 45 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7583 (mmtm) outliers start: 15 outliers final: 13 residues processed: 217 average time/residue: 0.3052 time to fit residues: 85.6427 Evaluate side-chains 223 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 347 SER Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.140784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119736 restraints weight = 34501.605| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.80 r_work: 0.3334 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9243 Z= 0.128 Angle : 0.461 5.263 12520 Z= 0.244 Chirality : 0.039 0.159 1417 Planarity : 0.004 0.046 1588 Dihedral : 3.848 17.482 1263 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.42 % Allowed : 13.33 % Favored : 85.25 % 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: 1.15 (0.26), residues: 1128 helix: 2.49 (0.26), residues: 415 sheet: -0.14 (0.32), residues: 263 loop : -0.27 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 97 TYR 0.022 0.001 TYR E 190 PHE 0.010 0.001 PHE E 79 TRP 0.011 0.001 TRP A 211 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9242) covalent geometry : angle 0.46061 (12518) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.35870 ( 2) hydrogen bonds : bond 0.03597 ( 442) hydrogen bonds : angle 4.11247 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 314 PHE cc_start: 0.7265 (t80) cc_final: 0.7009 (t80) REVERT: A 217 ASP cc_start: 0.6738 (t70) cc_final: 0.6401 (t0) REVERT: A 258 LEU cc_start: 0.7845 (mt) cc_final: 0.7549 (mp) REVERT: A 281 GLU cc_start: 0.6903 (tp30) cc_final: 0.6572 (tp30) REVERT: A 314 ASP cc_start: 0.7503 (t0) cc_final: 0.7193 (t0) REVERT: B 151 LEU cc_start: 0.7568 (mt) cc_final: 0.7342 (mt) REVERT: B 273 ASN cc_start: 0.7151 (t0) cc_final: 0.6842 (t0) REVERT: B 339 SER cc_start: 0.7904 (m) cc_final: 0.7450 (p) REVERT: E 88 GLU cc_start: 0.7224 (mp0) cc_final: 0.6862 (mp0) REVERT: E 160 ARG cc_start: 0.7287 (ttm-80) cc_final: 0.7048 (ttm-80) REVERT: E 213 THR cc_start: 0.8218 (m) cc_final: 0.7853 (p) REVERT: E 215 THR cc_start: 0.8089 (m) cc_final: 0.7628 (p) REVERT: G 20 MET cc_start: 0.7111 (mmm) cc_final: 0.6722 (mmm) REVERT: G 45 LYS cc_start: 0.7925 (mmtm) cc_final: 0.7556 (mmtm) outliers start: 14 outliers final: 13 residues processed: 225 average time/residue: 0.3177 time to fit residues: 91.4956 Evaluate side-chains 230 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 347 SER Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 0.0970 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120341 restraints weight = 34594.315| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.80 r_work: 0.3343 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9243 Z= 0.110 Angle : 0.446 4.853 12520 Z= 0.234 Chirality : 0.038 0.154 1417 Planarity : 0.003 0.041 1588 Dihedral : 3.704 16.762 1263 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 13.43 % Favored : 85.15 % 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: 1.30 (0.26), residues: 1128 helix: 2.67 (0.26), residues: 415 sheet: -0.12 (0.32), residues: 268 loop : -0.20 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 97 TYR 0.019 0.001 TYR E 190 PHE 0.010 0.001 PHE A 189 TRP 0.011 0.001 TRP A 211 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9242) covalent geometry : angle 0.44572 (12518) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.22628 ( 2) hydrogen bonds : bond 0.03414 ( 442) hydrogen bonds : angle 4.00864 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5503.36 seconds wall clock time: 94 minutes 26.42 seconds (5666.42 seconds total)