Starting phenix.real_space_refine on Sat Jun 14 19:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uhb_42268/06_2025/8uhb_42268_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uhb_42268/06_2025/8uhb_42268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uhb_42268/06_2025/8uhb_42268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uhb_42268/06_2025/8uhb_42268.map" model { file = "/net/cci-nas-00/data/ceres_data/8uhb_42268/06_2025/8uhb_42268_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uhb_42268/06_2025/8uhb_42268_trim.cif" } resolution = 3.35 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= 0.000 sd= 0.038 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 65 5.16 5 C 5346 2.51 5 N 1453 2.21 5 O 1553 1.98 5 H 8144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 16561 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4754 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5106 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3890 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 884 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1911 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'WV8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.02, per 1000 atoms: 0.48 Number of scatterers: 16561 At special positions: 0 Unit cell: (85.52, 100.486, 136.832, 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 65 16.00 O 1553 8.00 N 1453 7.00 C 5346 6.00 H 8144 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 13 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 4.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 39.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.835A pdb=" N ILE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 76 removed outlier: 3.918A pdb=" N ILE A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.556A pdb=" N SER A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 removed outlier: 3.686A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 126 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.506A pdb=" N LYS A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.954A pdb=" N CYS A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 199 through 228 removed outlier: 4.152A pdb=" N ARG A 212 " --> pdb=" O CYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 4.272A pdb=" N LYS A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 266 - end of helix removed outlier: 3.725A pdb=" N ASP A 274 " --> pdb=" O CYS A 270 " (cutoff:3.500A) Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 282 through 305 removed outlier: 3.693A pdb=" N ASN A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.761A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.677A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 38 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.526A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 334 through 353 removed outlier: 4.249A pdb=" N LYS C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 391 removed outlier: 3.951A pdb=" N VAL C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 383 " --> pdb=" O CYS C 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.532A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.673A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.986A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.984A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.617A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.715A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.809A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.471A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 209 Processing sheet with id=AB1, first strand: chain 'C' and resid 246 through 249 removed outlier: 7.020A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.502A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1113 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: 5.99 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8118 1.03 - 1.23: 141 1.23 - 1.43: 3560 1.43 - 1.62: 4828 1.62 - 1.82: 94 Bond restraints: 16741 Sorted by residual: bond pdb=" C8 WV8 A 401 " pdb=" N9 WV8 A 401 " ideal model delta sigma weight residual 1.359 1.326 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C MET A 77 " pdb=" O MET A 77 " ideal model delta sigma weight residual 1.244 1.231 0.013 1.00e-02 1.00e+04 1.60e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.30e-01 bond pdb=" C VAL A 250 " pdb=" O VAL A 250 " ideal model delta sigma weight residual 1.237 1.226 0.011 1.12e-02 7.97e+03 9.28e-01 bond pdb=" C8 WV8 A 401 " pdb=" O7 WV8 A 401 " ideal model delta sigma weight residual 1.361 1.344 0.017 2.00e-02 2.50e+03 6.90e-01 ... (remaining 16736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 27324 1.01 - 2.02: 2542 2.02 - 3.03: 149 3.03 - 4.04: 44 4.04 - 5.05: 14 Bond angle restraints: 30073 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.67 3.53 9.60e-01 1.09e+00 1.35e+01 angle pdb=" N ILE C 372 " pdb=" CA ILE C 372 " pdb=" C ILE C 372 " ideal model delta sigma weight residual 112.35 107.30 5.05 1.41e+00 5.03e-01 1.28e+01 angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 113.07 108.53 4.54 1.37e+00 5.33e-01 1.10e+01 angle pdb=" N ASP C 310 " pdb=" CA ASP C 310 " pdb=" C ASP C 310 " ideal model delta sigma weight residual 114.04 110.13 3.91 1.24e+00 6.50e-01 9.93e+00 angle pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" C VAL A 46 " ideal model delta sigma weight residual 111.45 108.65 2.80 9.30e-01 1.16e+00 9.06e+00 ... (remaining 30068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7184 17.66 - 35.32: 599 35.32 - 52.98: 135 52.98 - 70.64: 21 70.64 - 88.30: 9 Dihedral angle restraints: 7948 sinusoidal: 4200 harmonic: 3748 Sorted by residual: dihedral pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " pdb=" SG CYS A 178 " pdb=" CB CYS A 178 " ideal model delta sinusoidal sigma weight residual 93.00 175.02 -82.02 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual -86.00 -154.02 68.02 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CA ILE C 341 " pdb=" C ILE C 341 " pdb=" N ARG C 342 " pdb=" CA ARG C 342 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 7945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 787 0.032 - 0.064: 371 0.064 - 0.096: 94 0.096 - 0.128: 44 0.128 - 0.160: 8 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA ILE C 341 " pdb=" N ILE C 341 " pdb=" C ILE C 341 " pdb=" CB ILE C 341 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 46 " pdb=" CA VAL A 46 " pdb=" CG1 VAL A 46 " pdb=" CG2 VAL A 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE C 244 " pdb=" N ILE C 244 " pdb=" C ILE C 244 " pdb=" CB ILE C 244 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1301 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 WV8 A 401 " 0.048 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" C8 WV8 A 401 " -0.013 2.00e-02 2.50e+03 pdb=" N10 WV8 A 401 " -0.051 2.00e-02 2.50e+03 pdb=" N9 WV8 A 401 " 0.039 2.00e-02 2.50e+03 pdb=" O7 WV8 A 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.020 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" CG PHE B 234 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 234 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 281 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 282 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.026 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 262 2.06 - 2.69: 26322 2.69 - 3.33: 47799 3.33 - 3.96: 61919 3.96 - 4.60: 97889 Nonbonded interactions: 234191 Sorted by model distance: nonbonded pdb=" HE2 HIS C 362 " pdb=" OD2 ASP C 378 " model vdw 1.420 2.450 nonbonded pdb=" OD1 ASP C 331 " pdb=" H VAL C 334 " model vdw 1.525 2.450 nonbonded pdb=" OD1 ASP B 228 " pdb=" HH TYR N 117 " model vdw 1.564 2.450 nonbonded pdb=" O ARG B 68 " pdb=" HG SER B 84 " model vdw 1.606 2.450 nonbonded pdb="HH12 ARG N 67 " pdb=" OD2 ASP N 90 " model vdw 1.630 2.450 ... (remaining 234186 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: 1.270 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: 0.280 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 36.350 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 0.034 8602 Z= 0.172 Angle : 0.621 5.054 11653 Z= 0.368 Chirality : 0.041 0.160 1304 Planarity : 0.003 0.048 1482 Dihedral : 14.115 88.305 3086 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.42 (0.26), residues: 1059 helix: 0.13 (0.28), residues: 385 sheet: -1.84 (0.33), residues: 218 loop : -1.30 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.035 0.001 PHE B 234 TYR 0.013 0.001 TYR C 311 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.15593 ( 390) hydrogen bonds : angle 7.43436 ( 1113) SS BOND : bond 0.00167 ( 5) SS BOND : angle 1.80433 ( 10) covalent geometry : bond 0.00369 ( 8597) covalent geometry : angle 0.61901 (11643) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.303 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: 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 outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5943 time to fit residues: 136.6305 Evaluate side-chains 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 55 HIS B 16 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057485 restraints weight = 86125.313| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.32 r_work: 0.2911 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8602 Z= 0.130 Angle : 0.564 5.566 11653 Z= 0.307 Chirality : 0.040 0.136 1304 Planarity : 0.004 0.048 1482 Dihedral : 5.484 38.399 1183 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.33 % Allowed : 8.03 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.23 (0.26), residues: 1059 helix: 0.33 (0.27), residues: 400 sheet: -1.65 (0.33), residues: 222 loop : -1.31 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS C 362 PHE 0.018 0.001 PHE C 212 TYR 0.010 0.001 TYR B 59 ARG 0.004 0.000 ARG C 283 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 390) hydrogen bonds : angle 5.59293 ( 1113) SS BOND : bond 0.00157 ( 5) SS BOND : angle 1.20291 ( 10) covalent geometry : bond 0.00271 ( 8597) covalent geometry : angle 0.56290 (11643) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 1.306 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 279 ASN cc_start: 0.9731 (t0) cc_final: 0.9275 (t0) REVERT: G 21 MET cc_start: 0.9386 (ttt) cc_final: 0.9168 (ttm) REVERT: N 34 MET cc_start: 0.8795 (mmm) cc_final: 0.8424 (tpp) outliers start: 3 outliers final: 3 residues processed: 126 average time/residue: 0.5907 time to fit residues: 98.8472 Evaluate side-chains 115 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.070375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.054482 restraints weight = 87351.526| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.18 r_work: 0.2844 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8602 Z= 0.247 Angle : 0.584 5.913 11653 Z= 0.322 Chirality : 0.041 0.132 1304 Planarity : 0.004 0.040 1482 Dihedral : 5.222 34.439 1183 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.78 % Allowed : 9.14 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.98 (0.27), residues: 1059 helix: 0.53 (0.27), residues: 400 sheet: -1.44 (0.34), residues: 221 loop : -1.23 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS C 362 PHE 0.016 0.001 PHE B 234 TYR 0.011 0.001 TYR C 311 ARG 0.003 0.000 ARG C 336 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 390) hydrogen bonds : angle 5.28800 ( 1113) SS BOND : bond 0.00093 ( 5) SS BOND : angle 0.88248 ( 10) covalent geometry : bond 0.00515 ( 8597) covalent geometry : angle 0.58380 (11643) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.744 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 ASP cc_start: 0.9067 (m-30) cc_final: 0.8779 (t0) REVERT: C 60 MET cc_start: 0.8777 (mpp) cc_final: 0.8485 (mpp) REVERT: C 268 GLU cc_start: 0.8798 (pt0) cc_final: 0.8532 (pt0) REVERT: C 279 ASN cc_start: 0.9729 (t0) cc_final: 0.9253 (t0) REVERT: G 21 MET cc_start: 0.9391 (ttt) cc_final: 0.9127 (ttm) REVERT: N 34 MET cc_start: 0.8739 (mmm) cc_final: 0.8422 (mmm) outliers start: 7 outliers final: 5 residues processed: 119 average time/residue: 0.6162 time to fit residues: 98.0794 Evaluate side-chains 109 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 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 = 0.3397 r_free = 0.3397 target = 0.070534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.054669 restraints weight = 87131.601| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.18 r_work: 0.2857 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8602 Z= 0.161 Angle : 0.532 5.620 11653 Z= 0.290 Chirality : 0.040 0.135 1304 Planarity : 0.003 0.039 1482 Dihedral : 5.052 33.368 1183 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.78 % Allowed : 9.70 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.70 (0.27), residues: 1059 helix: 0.82 (0.27), residues: 401 sheet: -1.26 (0.34), residues: 215 loop : -1.17 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS C 362 PHE 0.016 0.001 PHE C 222 TYR 0.009 0.001 TYR C 358 ARG 0.003 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 390) hydrogen bonds : angle 5.07153 ( 1113) SS BOND : bond 0.00086 ( 5) SS BOND : angle 0.59763 ( 10) covalent geometry : bond 0.00337 ( 8597) covalent geometry : angle 0.53155 (11643) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.972 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: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.9309 (ppp) cc_final: 0.9101 (ppp) REVERT: B 230 ASN cc_start: 0.9420 (m-40) cc_final: 0.9074 (m110) REVERT: B 322 ASP cc_start: 0.9049 (m-30) cc_final: 0.8790 (t0) REVERT: C 15 GLU cc_start: 0.9487 (OUTLIER) cc_final: 0.9244 (tm-30) REVERT: G 21 MET cc_start: 0.9417 (ttt) cc_final: 0.9167 (ttm) REVERT: G 47 GLU cc_start: 0.8750 (mp0) cc_final: 0.8417 (mp0) REVERT: N 34 MET cc_start: 0.8779 (mmm) cc_final: 0.8378 (tpp) outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.5887 time to fit residues: 94.7849 Evaluate side-chains 109 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.054106 restraints weight = 88749.416| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.18 r_work: 0.2854 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8602 Z= 0.161 Angle : 0.529 5.046 11653 Z= 0.288 Chirality : 0.039 0.134 1304 Planarity : 0.003 0.038 1482 Dihedral : 4.863 33.942 1183 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.11 % Allowed : 10.81 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.46 (0.27), residues: 1059 helix: 1.11 (0.27), residues: 398 sheet: -1.05 (0.35), residues: 213 loop : -1.16 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 220 PHE 0.029 0.001 PHE C 222 TYR 0.008 0.001 TYR B 264 ARG 0.003 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 390) hydrogen bonds : angle 4.90914 ( 1113) SS BOND : bond 0.00095 ( 5) SS BOND : angle 0.57669 ( 10) covalent geometry : bond 0.00339 ( 8597) covalent geometry : angle 0.52901 (11643) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.385 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: symmetry clash REVERT: A 69 ASP cc_start: 0.9337 (m-30) cc_final: 0.9068 (t0) REVERT: B 138 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8549 (mm-30) REVERT: B 230 ASN cc_start: 0.9440 (m-40) cc_final: 0.9079 (m110) REVERT: B 322 ASP cc_start: 0.9050 (m-30) cc_final: 0.8783 (t0) REVERT: C 15 GLU cc_start: 0.9488 (OUTLIER) cc_final: 0.9268 (tm-30) REVERT: C 60 MET cc_start: 0.8564 (mpp) cc_final: 0.8284 (mpp) REVERT: G 21 MET cc_start: 0.9435 (ttt) cc_final: 0.9181 (ttm) REVERT: N 34 MET cc_start: 0.8789 (mmm) cc_final: 0.8342 (tpp) outliers start: 10 outliers final: 7 residues processed: 117 average time/residue: 0.5025 time to fit residues: 79.2023 Evaluate side-chains 112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053463 restraints weight = 88311.276| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.12 r_work: 0.2838 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8602 Z= 0.198 Angle : 0.538 5.034 11653 Z= 0.294 Chirality : 0.039 0.136 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.820 33.742 1183 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.23 % Allowed : 11.37 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.28 (0.27), residues: 1059 helix: 1.29 (0.27), residues: 401 sheet: -1.01 (0.35), residues: 215 loop : -1.07 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 357 PHE 0.027 0.001 PHE C 222 TYR 0.012 0.001 TYR A 200 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 390) hydrogen bonds : angle 4.87826 ( 1113) SS BOND : bond 0.00140 ( 5) SS BOND : angle 0.57281 ( 10) covalent geometry : bond 0.00413 ( 8597) covalent geometry : angle 0.53797 (11643) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.464 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: symmetry clash REVERT: B 262 MET cc_start: 0.8865 (ttm) cc_final: 0.8604 (ttm) REVERT: B 322 ASP cc_start: 0.9075 (m-30) cc_final: 0.8810 (t0) REVERT: C 60 MET cc_start: 0.8513 (mpp) cc_final: 0.8249 (mpp) REVERT: G 21 MET cc_start: 0.9401 (ttt) cc_final: 0.9145 (ttm) REVERT: N 34 MET cc_start: 0.8800 (mmm) cc_final: 0.8334 (tpp) REVERT: N 77 ASN cc_start: 0.9314 (m-40) cc_final: 0.8882 (p0) outliers start: 11 outliers final: 9 residues processed: 113 average time/residue: 0.5120 time to fit residues: 77.6293 Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.069467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053885 restraints weight = 87898.137| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.11 r_work: 0.2851 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8602 Z= 0.151 Angle : 0.529 5.989 11653 Z= 0.286 Chirality : 0.039 0.136 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.786 34.107 1183 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 1.45 % Allowed : 11.37 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.17 (0.27), residues: 1059 helix: 1.40 (0.27), residues: 398 sheet: -0.86 (0.35), residues: 213 loop : -1.08 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 357 PHE 0.020 0.001 PHE C 222 TYR 0.007 0.001 TYR C 318 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 390) hydrogen bonds : angle 4.78871 ( 1113) SS BOND : bond 0.00115 ( 5) SS BOND : angle 1.75201 ( 10) covalent geometry : bond 0.00321 ( 8597) covalent geometry : angle 0.52699 (11643) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.371 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 132 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9190 (mmmt) REVERT: B 262 MET cc_start: 0.8836 (ttm) cc_final: 0.8605 (ttm) REVERT: B 322 ASP cc_start: 0.9061 (m-30) cc_final: 0.8800 (t0) REVERT: C 60 MET cc_start: 0.8488 (mpp) cc_final: 0.8277 (mpp) REVERT: G 21 MET cc_start: 0.9389 (ttt) cc_final: 0.9136 (ttm) REVERT: N 34 MET cc_start: 0.8815 (mmm) cc_final: 0.8330 (tpp) REVERT: N 77 ASN cc_start: 0.9286 (m-40) cc_final: 0.8869 (p0) outliers start: 13 outliers final: 11 residues processed: 117 average time/residue: 0.5124 time to fit residues: 80.4816 Evaluate side-chains 115 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.070004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054486 restraints weight = 87902.389| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.16 r_work: 0.2867 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8602 Z= 0.112 Angle : 0.516 5.277 11653 Z= 0.277 Chirality : 0.039 0.139 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.686 34.649 1183 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.00 % Allowed : 12.26 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.03 (0.27), residues: 1059 helix: 1.52 (0.27), residues: 398 sheet: -0.70 (0.35), residues: 211 loop : -1.05 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS C 357 PHE 0.017 0.001 PHE C 222 TYR 0.008 0.001 TYR C 318 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 390) hydrogen bonds : angle 4.69830 ( 1113) SS BOND : bond 0.00174 ( 5) SS BOND : angle 1.31312 ( 10) covalent geometry : bond 0.00245 ( 8597) covalent geometry : angle 0.51523 (11643) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.592 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: A 69 ASP cc_start: 0.9419 (m-30) cc_final: 0.9198 (t0) REVERT: A 132 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9172 (mmmt) REVERT: B 230 ASN cc_start: 0.9389 (m-40) cc_final: 0.9099 (m110) REVERT: B 262 MET cc_start: 0.8796 (ttm) cc_final: 0.8574 (ttm) REVERT: B 322 ASP cc_start: 0.9020 (m-30) cc_final: 0.8766 (t0) REVERT: G 21 MET cc_start: 0.9409 (ttt) cc_final: 0.9167 (ttm) REVERT: G 47 GLU cc_start: 0.8946 (mp0) cc_final: 0.8532 (mp0) REVERT: N 34 MET cc_start: 0.8835 (mmm) cc_final: 0.8349 (tpp) REVERT: N 77 ASN cc_start: 0.9261 (m-40) cc_final: 0.8866 (p0) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 0.6867 time to fit residues: 109.9646 Evaluate side-chains 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 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 = 0.3380 r_free = 0.3380 target = 0.069117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053591 restraints weight = 88689.627| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.14 r_work: 0.2846 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8602 Z= 0.173 Angle : 0.547 7.826 11653 Z= 0.294 Chirality : 0.040 0.134 1304 Planarity : 0.003 0.036 1482 Dihedral : 4.694 34.426 1183 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.34 % Allowed : 12.60 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.01 (0.27), residues: 1059 helix: 1.55 (0.27), residues: 398 sheet: -0.64 (0.35), residues: 213 loop : -1.08 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS C 357 PHE 0.017 0.001 PHE C 222 TYR 0.012 0.001 TYR B 59 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 390) hydrogen bonds : angle 4.77201 ( 1113) SS BOND : bond 0.00239 ( 5) SS BOND : angle 1.01786 ( 10) covalent geometry : bond 0.00364 ( 8597) covalent geometry : angle 0.54637 (11643) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.166 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 30 MET cc_start: 0.9700 (mtp) cc_final: 0.9464 (mtm) REVERT: A 132 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9200 (mmmt) REVERT: B 230 ASN cc_start: 0.9435 (m-40) cc_final: 0.9090 (m110) REVERT: B 262 MET cc_start: 0.8830 (ttm) cc_final: 0.8621 (ttm) REVERT: B 322 ASP cc_start: 0.9034 (m-30) cc_final: 0.8783 (t0) REVERT: G 21 MET cc_start: 0.9407 (ttt) cc_final: 0.9165 (ttm) REVERT: G 47 GLU cc_start: 0.8938 (mp0) cc_final: 0.8520 (mp0) REVERT: N 34 MET cc_start: 0.8844 (mmm) cc_final: 0.8359 (tpp) REVERT: N 77 ASN cc_start: 0.9275 (m-40) cc_final: 0.8877 (p0) outliers start: 12 outliers final: 9 residues processed: 116 average time/residue: 0.5287 time to fit residues: 82.9452 Evaluate side-chains 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 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 = 0.3379 r_free = 0.3379 target = 0.068987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.053471 restraints weight = 88301.289| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.14 r_work: 0.2846 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8602 Z= 0.160 Angle : 0.542 7.725 11653 Z= 0.292 Chirality : 0.039 0.133 1304 Planarity : 0.003 0.036 1482 Dihedral : 4.690 34.627 1183 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.11 % Allowed : 12.71 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.00 (0.27), residues: 1059 helix: 1.59 (0.27), residues: 398 sheet: -0.66 (0.35), residues: 218 loop : -1.10 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS C 357 PHE 0.017 0.001 PHE C 222 TYR 0.008 0.001 TYR C 358 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 390) hydrogen bonds : angle 4.74727 ( 1113) SS BOND : bond 0.00216 ( 5) SS BOND : angle 0.95619 ( 10) covalent geometry : bond 0.00341 ( 8597) covalent geometry : angle 0.54133 (11643) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.401 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: A 132 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9195 (mmmt) REVERT: B 262 MET cc_start: 0.8836 (ttm) cc_final: 0.8632 (ttm) REVERT: B 322 ASP cc_start: 0.9012 (m-30) cc_final: 0.8764 (t0) REVERT: G 21 MET cc_start: 0.9405 (ttt) cc_final: 0.9164 (ttm) REVERT: G 47 GLU cc_start: 0.8933 (mp0) cc_final: 0.8511 (mp0) REVERT: N 34 MET cc_start: 0.8850 (mmm) cc_final: 0.8352 (tpp) REVERT: N 77 ASN cc_start: 0.9282 (m-40) cc_final: 0.8882 (p0) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.5488 time to fit residues: 87.2947 Evaluate side-chains 114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 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 = 0.3373 r_free = 0.3373 target = 0.068574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.053333 restraints weight = 89027.249| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.14 r_work: 0.2831 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8602 Z= 0.191 Angle : 0.561 7.704 11653 Z= 0.303 Chirality : 0.040 0.132 1304 Planarity : 0.003 0.036 1482 Dihedral : 4.739 34.583 1183 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.34 % Allowed : 12.71 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.07 (0.27), residues: 1059 helix: 1.41 (0.26), residues: 404 sheet: -0.71 (0.34), residues: 221 loop : -1.03 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS C 357 PHE 0.020 0.001 PHE C 222 TYR 0.009 0.001 TYR C 358 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 390) hydrogen bonds : angle 4.78770 ( 1113) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.83994 ( 10) covalent geometry : bond 0.00404 ( 8597) covalent geometry : angle 0.56045 (11643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7447.03 seconds wall clock time: 131 minutes 59.71 seconds (7919.71 seconds total)