Starting phenix.real_space_refine on Sun Jun 15 22:03:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibv_35346/06_2025/8ibv_35346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibv_35346/06_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_35346/06_2025/8ibv_35346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibv_35346/06_2025/8ibv_35346.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibv_35346/06_2025/8ibv_35346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibv_35346/06_2025/8ibv_35346.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.94, per 1000 atoms: 0.49 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: 4.75 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.52 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: 6.14 Time building geometry restraints manager: 5.78 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: 0.680 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: 0.330 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 40.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- 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 : 4.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.000 TRP E 110 HIS 0.001 0.000 HIS B 271 PHE 0.013 0.001 PHE R 231 TYR 0.009 0.000 TYR R 96 ARG 0.007 0.000 ARG R 233 Details of bonding type rmsd hydrogen bonds : bond 0.19133 ( 442) hydrogen bonds : angle 6.68340 ( 1272) SS BOND : bond 0.01577 ( 1) SS BOND : angle 3.08137 ( 2) covalent geometry : bond 0.00401 ( 9242) covalent geometry : angle 0.54811 (12518) *********************** 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 : 1.250 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: 0.6587 (ttm170) REVERT: A 275 ILE cc_start: 0.8025 (mt) cc_final: 0.7615 (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: 0.7672 (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: 0.7765 (m110) REVERT: E 42 LYS cc_start: 0.8024 (tptt) cc_final: 0.7789 (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: 0.5755 time to fit residues: 194.3949 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 : 1.380 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.148521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128385 restraints weight = 34968.953| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.81 r_work: 0.3473 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9243 Z= 0.202 Angle : 0.581 7.381 12520 Z= 0.303 Chirality : 0.043 0.204 1417 Planarity : 0.005 0.087 1588 Dihedral : 3.961 52.907 1265 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.53 % Allowed : 7.93 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1128 helix: 1.64 (0.25), residues: 410 sheet: -0.40 (0.30), residues: 268 loop : -0.75 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 337 HIS 0.007 0.002 HIS A 197 PHE 0.021 0.002 PHE R 314 TYR 0.031 0.002 TYR E 190 ARG 0.011 0.001 ARG R 233 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 442) hydrogen bonds : angle 4.48165 ( 1272) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.59006 ( 2) covalent geometry : bond 0.00473 ( 9242) covalent geometry : angle 0.58105 (12518) *********************** 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: 15 poor density : 254 time to evaluate : 1.380 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: A 188 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7671 (ttpp) REVERT: A 241 LYS cc_start: 0.8186 (tttp) cc_final: 0.7969 (ttmm) REVERT: A 247 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7460 (ttm170) REVERT: A 258 LEU cc_start: 0.7890 (mt) cc_final: 0.7597 (mp) REVERT: B 47 ARG cc_start: 0.6117 (mtm-85) cc_final: 0.5905 (mtm-85) REVERT: B 273 ASN cc_start: 0.7261 (t0) cc_final: 0.6914 (t0) REVERT: B 339 SER cc_start: 0.7720 (m) cc_final: 0.7264 (t) REVERT: E 42 LYS cc_start: 0.8186 (tptt) cc_final: 0.7942 (tptt) REVERT: E 86 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7411 (mtt180) REVERT: E 88 GLU cc_start: 0.7001 (mp0) cc_final: 0.6662 (mp0) REVERT: E 213 THR cc_start: 0.7843 (m) cc_final: 0.7488 (p) REVERT: E 215 THR cc_start: 0.7754 (m) cc_final: 0.7452 (p) REVERT: G 20 MET cc_start: 0.6937 (mmm) cc_final: 0.6600 (mmm) REVERT: G 45 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7628 (mmtm) outliers start: 15 outliers final: 13 residues processed: 262 average time/residue: 0.6559 time to fit residues: 229.0991 Evaluate side-chains 252 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain R residue 341 LEU 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 B residue 42 ILE Chi-restraints excluded: chain B residue 189 THR 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 59 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** R 356 ASN 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 = 0.3774 r_free = 0.3774 target = 0.143249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122287 restraints weight = 34835.927| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.85 r_work: 0.3370 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9243 Z= 0.220 Angle : 0.516 5.968 12520 Z= 0.278 Chirality : 0.041 0.173 1417 Planarity : 0.004 0.047 1588 Dihedral : 3.824 16.126 1263 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.73 % Allowed : 9.97 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1128 helix: 1.83 (0.25), residues: 415 sheet: -0.31 (0.30), residues: 285 loop : -0.52 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 216 HIS 0.009 0.002 HIS E 232 PHE 0.021 0.002 PHE R 314 TYR 0.028 0.002 TYR E 190 ARG 0.005 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 442) hydrogen bonds : angle 4.34701 ( 1272) SS BOND : bond 0.00282 ( 1) SS BOND : angle 0.59584 ( 2) covalent geometry : bond 0.00514 ( 9242) covalent geometry : angle 0.51642 (12518) *********************** 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 246 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 1.265 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: A 188 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7674 (ttpp) REVERT: A 247 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7537 (ttm170) REVERT: A 314 ASP cc_start: 0.7640 (t0) cc_final: 0.7309 (t0) REVERT: B 160 ASN cc_start: 0.8242 (t0) cc_final: 0.8013 (t0) REVERT: B 273 ASN cc_start: 0.7198 (t0) cc_final: 0.6867 (t0) REVERT: B 339 SER cc_start: 0.7899 (m) cc_final: 0.7436 (t) REVERT: E 86 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7546 (mtt180) REVERT: E 88 GLU cc_start: 0.7188 (mp0) cc_final: 0.6846 (mp0) REVERT: E 213 THR cc_start: 0.8016 (m) cc_final: 0.7627 (p) REVERT: E 215 THR cc_start: 0.7949 (m) cc_final: 0.7507 (p) REVERT: G 20 MET cc_start: 0.6991 (mmm) cc_final: 0.6638 (mmm) REVERT: G 45 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7616 (mmtm) outliers start: 17 outliers final: 12 residues processed: 236 average time/residue: 0.5650 time to fit residues: 175.3713 Evaluate side-chains 233 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 R residue 349 SER Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 191 VAL 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 E residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120755 restraints weight = 35079.885| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.86 r_work: 0.3353 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9243 Z= 0.177 Angle : 0.484 5.797 12520 Z= 0.257 Chirality : 0.040 0.169 1417 Planarity : 0.004 0.045 1588 Dihedral : 3.821 17.446 1263 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 10.99 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1128 helix: 2.07 (0.25), residues: 412 sheet: -0.29 (0.31), residues: 273 loop : -0.42 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.011 0.002 HIS A 324 PHE 0.014 0.001 PHE R 314 TYR 0.027 0.001 TYR E 190 ARG 0.006 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 442) hydrogen bonds : angle 4.21208 ( 1272) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.52311 ( 2) covalent geometry : bond 0.00408 ( 9242) covalent geometry : angle 0.48431 (12518) *********************** 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 234 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.393 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: R 248 MET cc_start: 0.6732 (tmm) cc_final: 0.6393 (tmm) REVERT: A 247 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7539 (ttm170) REVERT: A 314 ASP cc_start: 0.7616 (t0) cc_final: 0.7309 (t0) REVERT: B 273 ASN cc_start: 0.7211 (t0) cc_final: 0.6894 (t0) REVERT: B 339 SER cc_start: 0.7934 (m) cc_final: 0.7469 (t) REVERT: E 88 GLU cc_start: 0.7233 (mp0) cc_final: 0.6888 (mp0) REVERT: E 140 MET cc_start: 0.8505 (mmm) cc_final: 0.6548 (mmm) REVERT: E 213 THR cc_start: 0.8072 (m) cc_final: 0.7707 (p) REVERT: E 215 THR cc_start: 0.7966 (m) cc_final: 0.7513 (p) REVERT: G 20 MET cc_start: 0.7001 (mmm) cc_final: 0.6615 (mmm) REVERT: G 45 LYS cc_start: 0.7938 (mmtm) cc_final: 0.7581 (mmtm) outliers start: 18 outliers final: 10 residues processed: 224 average time/residue: 0.5905 time to fit residues: 171.8688 Evaluate side-chains 219 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.139465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118418 restraints weight = 34768.685| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.85 r_work: 0.3309 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9243 Z= 0.300 Angle : 0.564 6.997 12520 Z= 0.300 Chirality : 0.044 0.200 1417 Planarity : 0.004 0.055 1588 Dihedral : 4.275 20.604 1263 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.14 % Allowed : 11.50 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1128 helix: 1.77 (0.25), residues: 412 sheet: -0.17 (0.31), residues: 271 loop : -0.46 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.008 0.003 HIS B 147 PHE 0.027 0.002 PHE E 67 TYR 0.034 0.002 TYR E 190 ARG 0.005 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 442) hydrogen bonds : angle 4.52070 ( 1272) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.72354 ( 2) covalent geometry : bond 0.00708 ( 9242) covalent geometry : angle 0.56442 (12518) *********************** 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 224 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.243 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: C 9 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 314 ASP cc_start: 0.7415 (t0) cc_final: 0.7099 (t0) REVERT: A 348 ASP cc_start: 0.7753 (t70) cc_final: 0.7536 (t70) REVERT: B 47 ARG cc_start: 0.6479 (mtm-85) cc_final: 0.6237 (mmm-85) REVERT: B 273 ASN cc_start: 0.7166 (t0) cc_final: 0.6830 (t0) REVERT: B 339 SER cc_start: 0.8045 (m) cc_final: 0.7667 (p) REVERT: E 4 VAL cc_start: 0.7864 (m) cc_final: 0.7662 (p) REVERT: E 88 GLU cc_start: 0.7286 (mp0) cc_final: 0.6939 (mp0) REVERT: G 20 MET cc_start: 0.7154 (mmm) cc_final: 0.6746 (mmm) REVERT: G 45 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7585 (mmtm) outliers start: 21 outliers final: 15 residues processed: 211 average time/residue: 0.6289 time to fit residues: 171.4868 Evaluate side-chains 215 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 114 SER 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 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 299 CYS 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 92 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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** ** R 351 ASN ** 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 = 0.3730 r_free = 0.3730 target = 0.140095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118986 restraints weight = 34724.790| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.84 r_work: 0.3318 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9243 Z= 0.211 Angle : 0.508 5.701 12520 Z= 0.270 Chirality : 0.040 0.168 1417 Planarity : 0.004 0.054 1588 Dihedral : 4.149 20.575 1263 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 13.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1128 helix: 2.01 (0.25), residues: 415 sheet: -0.13 (0.32), residues: 271 loop : -0.37 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 216 HIS 0.019 0.002 HIS A 324 PHE 0.017 0.002 PHE R 314 TYR 0.029 0.002 TYR E 190 ARG 0.006 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 442) hydrogen bonds : angle 4.38655 ( 1272) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.62321 ( 2) covalent geometry : bond 0.00493 ( 9242) covalent geometry : angle 0.50755 (12518) *********************** 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: 16 poor density : 209 time to evaluate : 1.397 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: R 248 MET cc_start: 0.6464 (tmm) cc_final: 0.6124 (tmm) REVERT: C 9 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6774 (mt-10) REVERT: A 314 ASP cc_start: 0.7482 (t0) cc_final: 0.7176 (t0) REVERT: B 47 ARG cc_start: 0.6470 (mtm-85) cc_final: 0.6210 (mmm-85) REVERT: B 273 ASN cc_start: 0.7169 (t0) cc_final: 0.6877 (t0) REVERT: B 339 SER cc_start: 0.8018 (m) cc_final: 0.7620 (p) REVERT: E 88 GLU cc_start: 0.7334 (mp0) cc_final: 0.6980 (mp0) REVERT: E 115 THR cc_start: 0.8552 (t) cc_final: 0.8076 (p) REVERT: E 160 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.7078 (ttm-80) REVERT: E 215 THR cc_start: 0.8158 (m) cc_final: 0.7596 (p) REVERT: G 20 MET cc_start: 0.7181 (mmm) cc_final: 0.6773 (mmm) REVERT: G 45 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7592 (mmtm) outliers start: 16 outliers final: 14 residues processed: 216 average time/residue: 0.6174 time to fit residues: 171.3440 Evaluate side-chains 221 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** R 351 ASN ** 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 = 0.3735 r_free = 0.3735 target = 0.140339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119307 restraints weight = 34618.192| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.82 r_work: 0.3331 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9243 Z= 0.167 Angle : 0.484 5.399 12520 Z= 0.255 Chirality : 0.039 0.156 1417 Planarity : 0.004 0.050 1588 Dihedral : 3.992 20.035 1263 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.22 % Allowed : 14.04 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1128 helix: 2.25 (0.25), residues: 415 sheet: -0.04 (0.32), residues: 258 loop : -0.35 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.010 0.001 HIS A 324 PHE 0.019 0.001 PHE E 67 TYR 0.025 0.001 TYR E 190 ARG 0.006 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 442) hydrogen bonds : angle 4.26422 ( 1272) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.53131 ( 2) covalent geometry : bond 0.00389 ( 9242) covalent geometry : angle 0.48428 (12518) *********************** 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 230 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 1.272 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: R 248 MET cc_start: 0.6417 (tmm) cc_final: 0.6075 (tmm) REVERT: C 9 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 260 LYS cc_start: 0.8365 (mttm) cc_final: 0.8117 (mttp) REVERT: A 314 ASP cc_start: 0.7463 (t0) cc_final: 0.7156 (t0) REVERT: B 47 ARG cc_start: 0.6464 (mtm-85) cc_final: 0.6233 (mmm-85) REVERT: B 273 ASN cc_start: 0.7156 (t0) cc_final: 0.6853 (t0) REVERT: B 339 SER cc_start: 0.7976 (m) cc_final: 0.7562 (p) REVERT: E 88 GLU cc_start: 0.7298 (mp0) cc_final: 0.6941 (mp0) REVERT: E 115 THR cc_start: 0.8538 (t) cc_final: 0.8062 (p) REVERT: E 160 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.7072 (ttm-80) REVERT: E 215 THR cc_start: 0.8140 (m) cc_final: 0.7619 (p) REVERT: G 20 MET cc_start: 0.7157 (mmm) cc_final: 0.6752 (mmm) REVERT: G 45 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7546 (mmtm) outliers start: 12 outliers final: 11 residues processed: 225 average time/residue: 0.6067 time to fit residues: 178.1180 Evaluate side-chains 225 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain R residue 341 LEU 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 108 CYS Chi-restraints excluded: chain B residue 119 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 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118700 restraints weight = 34307.862| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.79 r_work: 0.3320 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9243 Z= 0.202 Angle : 0.501 5.333 12520 Z= 0.265 Chirality : 0.040 0.166 1417 Planarity : 0.004 0.050 1588 Dihedral : 4.077 20.562 1263 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 13.53 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1128 helix: 2.22 (0.25), residues: 415 sheet: -0.08 (0.32), residues: 260 loop : -0.28 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.006 0.001 HIS B 147 PHE 0.020 0.002 PHE R 314 TYR 0.028 0.001 TYR E 190 ARG 0.007 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 442) hydrogen bonds : angle 4.30480 ( 1272) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.57018 ( 2) covalent geometry : bond 0.00473 ( 9242) covalent geometry : angle 0.50060 (12518) *********************** 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 230 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 1.337 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: 0.6410 (tmm) cc_final: 0.6064 (tmm) REVERT: C 9 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6755 (mt-10) REVERT: A 217 ASP cc_start: 0.6833 (t70) cc_final: 0.6497 (t0) REVERT: A 260 LYS cc_start: 0.8348 (mttm) cc_final: 0.8096 (mttp) REVERT: A 314 ASP cc_start: 0.7442 (t0) cc_final: 0.7131 (t0) REVERT: B 47 ARG cc_start: 0.6499 (mtm-85) cc_final: 0.6263 (mmm-85) REVERT: B 273 ASN cc_start: 0.7150 (t0) cc_final: 0.6851 (t0) REVERT: B 339 SER cc_start: 0.7996 (m) cc_final: 0.7585 (p) REVERT: E 88 GLU cc_start: 0.7274 (mp0) cc_final: 0.6922 (mp0) REVERT: E 160 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.7066 (ttm-80) REVERT: E 215 THR cc_start: 0.8145 (m) cc_final: 0.7658 (p) REVERT: G 20 MET cc_start: 0.7185 (mmm) cc_final: 0.6796 (mmm) REVERT: G 45 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7576 (mmtm) outliers start: 19 outliers final: 17 residues processed: 221 average time/residue: 0.5752 time to fit residues: 165.7249 Evaluate side-chains 227 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 347 SER 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 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 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 351 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.140406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119349 restraints weight = 34683.702| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.81 r_work: 0.3336 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9243 Z= 0.132 Angle : 0.463 5.062 12520 Z= 0.244 Chirality : 0.039 0.156 1417 Planarity : 0.004 0.046 1588 Dihedral : 3.894 19.497 1263 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.73 % Allowed : 13.94 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1128 helix: 2.45 (0.26), residues: 415 sheet: -0.01 (0.32), residues: 258 loop : -0.24 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.004 0.001 HIS A 324 PHE 0.021 0.001 PHE E 67 TYR 0.021 0.001 TYR E 190 ARG 0.006 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 442) hydrogen bonds : angle 4.16422 ( 1272) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.38924 ( 2) covalent geometry : bond 0.00303 ( 9242) covalent geometry : angle 0.46282 (12518) *********************** 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 234 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 1.249 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: C 9 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6735 (mt-10) REVERT: A 217 ASP cc_start: 0.6801 (t70) cc_final: 0.6448 (t0) REVERT: A 258 LEU cc_start: 0.7863 (mt) cc_final: 0.7560 (mp) REVERT: A 260 LYS cc_start: 0.8366 (mttm) cc_final: 0.8107 (mttp) REVERT: A 314 ASP cc_start: 0.7427 (t0) cc_final: 0.7124 (t0) REVERT: A 323 ARG cc_start: 0.7071 (mtm110) cc_final: 0.6847 (mtm110) REVERT: B 47 ARG cc_start: 0.6500 (mtm-85) cc_final: 0.6246 (mmm-85) REVERT: B 273 ASN cc_start: 0.7098 (t0) cc_final: 0.6792 (t0) REVERT: B 339 SER cc_start: 0.7912 (m) cc_final: 0.7478 (p) REVERT: E 140 MET cc_start: 0.8446 (mmm) cc_final: 0.8240 (mmm) REVERT: E 160 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.7039 (ttm-80) REVERT: E 178 LEU cc_start: 0.8530 (tt) cc_final: 0.8285 (tp) REVERT: E 213 THR cc_start: 0.8315 (m) cc_final: 0.7894 (p) REVERT: E 215 THR cc_start: 0.8134 (m) cc_final: 0.7673 (p) REVERT: G 20 MET cc_start: 0.7151 (mmm) cc_final: 0.6757 (mmm) REVERT: G 45 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7543 (mmtm) outliers start: 17 outliers final: 14 residues processed: 225 average time/residue: 0.6179 time to fit residues: 181.9200 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 : 1.248 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain R residue 341 LEU 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 55 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** 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 = 0.3717 r_free = 0.3717 target = 0.138920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117999 restraints weight = 34493.667| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.79 r_work: 0.3305 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9243 Z= 0.295 Angle : 0.556 6.504 12520 Z= 0.296 Chirality : 0.043 0.188 1417 Planarity : 0.004 0.054 1588 Dihedral : 4.293 20.856 1263 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.63 % Allowed : 14.14 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1128 helix: 1.98 (0.25), residues: 417 sheet: -0.06 (0.32), residues: 259 loop : -0.34 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 216 HIS 0.006 0.002 HIS B 147 PHE 0.027 0.002 PHE R 314 TYR 0.034 0.002 TYR E 190 ARG 0.007 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 442) hydrogen bonds : angle 4.48361 ( 1272) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.70438 ( 2) covalent geometry : bond 0.00695 ( 9242) covalent geometry : angle 0.55559 (12518) ********************** 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 228 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 1.294 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: R 82 VAL cc_start: 0.7568 (OUTLIER) cc_final: 0.7125 (m) REVERT: A 31 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7057 (mtt-85) REVERT: A 217 ASP cc_start: 0.6918 (t70) cc_final: 0.6583 (t0) REVERT: A 314 ASP cc_start: 0.7398 (t0) cc_final: 0.7094 (t0) REVERT: A 323 ARG cc_start: 0.7060 (mtm110) cc_final: 0.6815 (mtm110) REVERT: B 47 ARG cc_start: 0.6531 (mtm-85) cc_final: 0.6286 (mmm-85) REVERT: B 273 ASN cc_start: 0.7151 (t0) cc_final: 0.6845 (t0) REVERT: B 339 SER cc_start: 0.8049 (m) cc_final: 0.7669 (p) REVERT: E 88 GLU cc_start: 0.7357 (mp0) cc_final: 0.7004 (mp0) REVERT: E 160 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.7069 (ttm-80) REVERT: E 215 THR cc_start: 0.8160 (m) cc_final: 0.7685 (p) REVERT: G 20 MET cc_start: 0.7237 (mmm) cc_final: 0.6829 (mmm) REVERT: G 45 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7537 (mmtm) outliers start: 16 outliers final: 12 residues processed: 219 average time/residue: 0.5706 time to fit residues: 164.5440 Evaluate side-chains 222 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 347 SER Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 ARG 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 55 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 96 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120351 restraints weight = 34670.763| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.84 r_work: 0.3342 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9243 Z= 0.110 Angle : 0.466 5.042 12520 Z= 0.244 Chirality : 0.038 0.160 1417 Planarity : 0.004 0.047 1588 Dihedral : 3.931 19.670 1263 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 14.95 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1128 helix: 2.41 (0.26), residues: 417 sheet: 0.06 (0.32), residues: 256 loop : -0.27 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.004 0.001 HIS A 324 PHE 0.023 0.001 PHE E 67 TYR 0.019 0.001 TYR E 190 ARG 0.006 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 442) hydrogen bonds : angle 4.19454 ( 1272) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.44399 ( 2) covalent geometry : bond 0.00247 ( 9242) covalent geometry : angle 0.46575 (12518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10769.05 seconds wall clock time: 184 minutes 41.34 seconds (11081.34 seconds total)