Starting phenix.real_space_refine on Mon Apr 28 20:13:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gyo_51700/04_2025/9gyo_51700.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gyo_51700/04_2025/9gyo_51700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gyo_51700/04_2025/9gyo_51700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gyo_51700/04_2025/9gyo_51700.map" model { file = "/net/cci-nas-00/data/ceres_data/9gyo_51700/04_2025/9gyo_51700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gyo_51700/04_2025/9gyo_51700.cif" } resolution = 2.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5146 2.51 5 N 1414 2.21 5 O 1480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8087 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1899 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2057 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 251} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CLR': 3, 'FWX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.84, per 1000 atoms: 0.60 Number of scatterers: 8087 At special positions: 0 Unit cell: (73.831, 97.223, 130.849, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1480 8.00 N 1414 7.00 C 5146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.43 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.15 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " 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: 1.84 Conformation dependent library (CDL) restraints added in 871.5 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.788A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.585A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.674A pdb=" N ASN A 218 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.536A pdb=" N LEU A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.632A pdb=" N ALA A 295 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 331 removed outlier: 3.623A pdb=" N PHE A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 370 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.759A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.598A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.868A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 42 removed outlier: 3.532A pdb=" N LEU R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 68 Processing helix chain 'R' and resid 70 through 75 removed outlier: 3.921A pdb=" N TRP R 75 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 116 Proline residue: R 92 - end of helix removed outlier: 3.543A pdb=" N ARG R 116 " --> pdb=" O MET R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 140 Proline residue: R 135 - end of helix Processing helix chain 'R' and resid 141 through 144 Processing helix chain 'R' and resid 156 through 161 removed outlier: 3.533A pdb=" N ILE R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 173 Processing helix chain 'R' and resid 173 through 207 removed outlier: 4.132A pdb=" N VAL R 206 " --> pdb=" O LEU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 235 Processing helix chain 'R' and resid 236 through 252 removed outlier: 3.522A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 275 Processing helix chain 'R' and resid 275 through 284 Processing helix chain 'R' and resid 284 through 289 Processing helix chain 'R' and resid 290 through 292 No H-bonds generated for 'chain 'R' and resid 290 through 292' Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.538A pdb=" N PHE A 191 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG A 35 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE A 224 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 37 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 226 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 39 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ALA A 228 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 223 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE A 269 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 225 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN A 271 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL A 227 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.689A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.544A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.834A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.178A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.892A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.596A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.131A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.754A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1194 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: 2.15 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2035 1.34 - 1.46: 2473 1.46 - 1.58: 3692 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 8265 Sorted by residual: bond pdb=" C SER R 47 " pdb=" N PRO R 48 " ideal model delta sigma weight residual 1.331 1.360 -0.028 8.70e-03 1.32e+04 1.06e+01 bond pdb=" CE1 HIS B 62 " pdb=" NE2 HIS B 62 " ideal model delta sigma weight residual 1.321 1.295 0.026 1.00e-02 1.00e+04 6.58e+00 bond pdb=" CA PRO R 48 " pdb=" C PRO R 48 " ideal model delta sigma weight residual 1.514 1.528 -0.014 5.50e-03 3.31e+04 6.19e+00 bond pdb=" C ARG R 254 " pdb=" N PRO R 255 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.18e-02 7.18e+03 5.25e+00 bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.534 1.495 0.039 1.77e-02 3.19e+03 4.95e+00 ... (remaining 8260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 9738 1.75 - 3.49: 1370 3.49 - 5.24: 119 5.24 - 6.98: 8 6.98 - 8.73: 3 Bond angle restraints: 11238 Sorted by residual: angle pdb=" NE ARG A 326 " pdb=" CZ ARG A 326 " pdb=" NH2 ARG A 326 " ideal model delta sigma weight residual 119.20 114.90 4.30 9.00e-01 1.23e+00 2.29e+01 angle pdb=" CA ASP B 323 " pdb=" CB ASP B 323 " pdb=" CG ASP B 323 " ideal model delta sigma weight residual 112.60 116.96 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CA ASP G 48 " pdb=" CB ASP G 48 " pdb=" CG ASP G 48 " ideal model delta sigma weight residual 112.60 116.90 -4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" N THR B 196 " pdb=" CA THR B 196 " pdb=" CB THR B 196 " ideal model delta sigma weight residual 114.17 109.48 4.69 1.14e+00 7.69e-01 1.69e+01 angle pdb=" CA THR N 111 " pdb=" CB THR N 111 " pdb=" OG1 THR N 111 " ideal model delta sigma weight residual 109.60 103.51 6.09 1.50e+00 4.44e-01 1.65e+01 ... (remaining 11233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 4459 14.99 - 29.97: 432 29.97 - 44.96: 117 44.96 - 59.95: 27 59.95 - 74.94: 34 Dihedral angle restraints: 5069 sinusoidal: 2101 harmonic: 2968 Sorted by residual: dihedral pdb=" CD ARG A 326 " pdb=" NE ARG A 326 " pdb=" CZ ARG A 326 " pdb=" NH1 ARG A 326 " ideal model delta sinusoidal sigma weight residual 0.00 72.49 -72.49 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 729 0.043 - 0.086: 339 0.086 - 0.129: 166 0.129 - 0.173: 31 0.173 - 0.216: 4 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PRO R 142 " pdb=" N PRO R 142 " pdb=" C PRO R 142 " pdb=" CB PRO R 142 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA PRO N 88 " pdb=" N PRO N 88 " pdb=" C PRO N 88 " pdb=" CB PRO N 88 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 1266 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 326 " -0.972 9.50e-02 1.11e+02 4.36e-01 1.24e+02 pdb=" NE ARG A 326 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 326 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 326 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 326 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 FWX R 401 " 0.056 2.00e-02 2.50e+03 5.02e-02 3.78e+01 pdb=" C10 FWX R 401 " -0.064 2.00e-02 2.50e+03 pdb=" C12 FWX R 401 " 0.013 2.00e-02 2.50e+03 pdb=" C14 FWX R 401 " -0.064 2.00e-02 2.50e+03 pdb=" N09 FWX R 401 " -0.002 2.00e-02 2.50e+03 pdb=" O13 FWX R 401 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.024 2.00e-02 2.50e+03 1.33e-02 4.42e+00 pdb=" CG TRP B 99 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.015 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 212 2.69 - 3.24: 7301 3.24 - 3.80: 12706 3.80 - 4.35: 18006 4.35 - 4.90: 29267 Nonbonded interactions: 67492 Sorted by model distance: nonbonded pdb=" OG1 THR B 321 " pdb=" O ASP B 323 " model vdw 2.139 3.040 nonbonded pdb=" NH1 ARG A 207 " pdb=" OD1 ASP B 186 " model vdw 2.272 3.120 nonbonded pdb=" O LEU R 74 " pdb=" OH TYR R 89 " model vdw 2.369 3.040 nonbonded pdb=" O THR N 113 " pdb=" NH2 ARG N 118 " model vdw 2.416 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.435 3.040 ... (remaining 67487 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.009 0.400 8268 Z= 0.531 Angle : 1.202 10.753 11244 Z= 0.814 Chirality : 0.059 0.216 1269 Planarity : 0.013 0.436 1425 Dihedral : 14.414 74.935 3146 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.23), residues: 1014 helix: -0.23 (0.22), residues: 395 sheet: -0.29 (0.29), residues: 228 loop : -1.63 (0.27), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP B 99 HIS 0.012 0.003 HIS B 62 PHE 0.014 0.003 PHE N 68 TYR 0.012 0.003 TYR B 85 ARG 0.051 0.002 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.22347 ( 421) hydrogen bonds : angle 7.63210 ( 1194) SS BOND : bond 0.24155 ( 3) SS BOND : angle 5.67578 ( 6) covalent geometry : bond 0.00750 ( 8265) covalent geometry : angle 1.19562 (11238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.938 Fit side-chains REVERT: A 21 LYS cc_start: 0.8150 (mttp) cc_final: 0.7467 (tmmt) REVERT: A 244 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7891 (tpt-90) REVERT: A 290 TYR cc_start: 0.7444 (m-80) cc_final: 0.7228 (m-10) REVERT: A 296 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7769 (mtm110) REVERT: A 365 MET cc_start: 0.8343 (ttm) cc_final: 0.8136 (ttp) REVERT: B 9 GLN cc_start: 0.7232 (mt0) cc_final: 0.6783 (tp40) REVERT: B 23 LYS cc_start: 0.8171 (tttp) cc_final: 0.7944 (tttp) REVERT: B 42 ARG cc_start: 0.7384 (tpt170) cc_final: 0.7052 (mmm160) REVERT: B 96 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7840 (mtm-85) REVERT: B 132 ASN cc_start: 0.5488 (OUTLIER) cc_final: 0.4659 (p0) REVERT: B 135 VAL cc_start: 0.8526 (t) cc_final: 0.8177 (p) REVERT: N 3 GLN cc_start: 0.8119 (mt0) cc_final: 0.7886 (mt0) REVERT: R 263 LEU cc_start: 0.6526 (mm) cc_final: 0.6072 (tp) outliers start: 6 outliers final: 1 residues processed: 143 average time/residue: 1.5639 time to fit residues: 234.0219 Evaluate side-chains 119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 132 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 257 ASN A 350 ASN B 17 GLN B 176 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106746 restraints weight = 8133.719| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.55 r_work: 0.2969 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8268 Z= 0.124 Angle : 0.558 7.493 11244 Z= 0.293 Chirality : 0.041 0.178 1269 Planarity : 0.004 0.032 1425 Dihedral : 6.069 49.001 1334 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.54 % Allowed : 10.99 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.25), residues: 1014 helix: 1.88 (0.25), residues: 405 sheet: 0.04 (0.33), residues: 210 loop : -1.07 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 213 HIS 0.007 0.001 HIS A 336 PHE 0.013 0.001 PHE N 29 TYR 0.014 0.001 TYR A 318 ARG 0.006 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 421) hydrogen bonds : angle 4.84965 ( 1194) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.87970 ( 6) covalent geometry : bond 0.00257 ( 8265) covalent geometry : angle 0.55754 (11238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.842 Fit side-chains REVERT: A 21 LYS cc_start: 0.8163 (mttp) cc_final: 0.7507 (tmmt) REVERT: A 195 LYS cc_start: 0.7785 (mmtp) cc_final: 0.7580 (mttm) REVERT: A 244 ARG cc_start: 0.8352 (mmm160) cc_final: 0.7500 (ttt-90) REVERT: A 247 GLU cc_start: 0.8586 (tt0) cc_final: 0.7848 (mm-30) REVERT: A 290 TYR cc_start: 0.7724 (m-80) cc_final: 0.7342 (m-80) REVERT: A 296 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7746 (mtm110) REVERT: A 352 ARG cc_start: 0.8334 (mmm160) cc_final: 0.8107 (tpp-160) REVERT: B 9 GLN cc_start: 0.7033 (mt0) cc_final: 0.6643 (tp40) REVERT: B 42 ARG cc_start: 0.7071 (tpt170) cc_final: 0.6761 (mmm160) REVERT: B 59 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.7918 (t80) REVERT: B 135 VAL cc_start: 0.8762 (t) cc_final: 0.8384 (p) REVERT: B 215 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: G 47 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7450 (mt-10) REVERT: N 3 GLN cc_start: 0.8438 (mt0) cc_final: 0.8009 (mt0) REVERT: N 111 THR cc_start: 0.8728 (m) cc_final: 0.8253 (p) REVERT: N 120 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: R 198 ASP cc_start: 0.8362 (m-30) cc_final: 0.8084 (m-30) REVERT: R 249 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7639 (tp) outliers start: 13 outliers final: 1 residues processed: 136 average time/residue: 1.4452 time to fit residues: 206.8330 Evaluate side-chains 120 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 61 optimal weight: 0.0060 chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 17 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105115 restraints weight = 8533.877| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.47 r_work: 0.2828 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8268 Z= 0.256 Angle : 0.709 10.777 11244 Z= 0.370 Chirality : 0.047 0.194 1269 Planarity : 0.006 0.053 1425 Dihedral : 7.035 59.836 1331 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.96 % Allowed : 12.53 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1014 helix: 1.90 (0.25), residues: 412 sheet: 0.29 (0.34), residues: 213 loop : -0.81 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 213 HIS 0.014 0.002 HIS B 62 PHE 0.022 0.002 PHE N 29 TYR 0.014 0.002 TYR A 318 ARG 0.010 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05752 ( 421) hydrogen bonds : angle 5.01232 ( 1194) SS BOND : bond 0.00733 ( 3) SS BOND : angle 1.58136 ( 6) covalent geometry : bond 0.00577 ( 8265) covalent geometry : angle 0.70775 (11238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.831 Fit side-chains REVERT: A 21 LYS cc_start: 0.8146 (mttp) cc_final: 0.7374 (tmmt) REVERT: A 195 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7691 (mttm) REVERT: A 247 GLU cc_start: 0.8553 (tt0) cc_final: 0.7709 (mm-30) REVERT: A 352 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8163 (tpp-160) REVERT: B 9 GLN cc_start: 0.7323 (mt0) cc_final: 0.6432 (mm-40) REVERT: B 59 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.8334 (t80) REVERT: B 112 VAL cc_start: 0.9058 (t) cc_final: 0.8847 (m) REVERT: B 132 ASN cc_start: 0.5808 (OUTLIER) cc_final: 0.4792 (p0) REVERT: B 135 VAL cc_start: 0.8839 (t) cc_final: 0.8530 (p) REVERT: B 215 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: B 217 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8323 (pmm) REVERT: G 47 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7548 (mt-10) REVERT: N 3 GLN cc_start: 0.8425 (mt0) cc_final: 0.7965 (mt0) REVERT: N 111 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8452 (p) REVERT: N 120 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: R 104 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8429 (mp) REVERT: R 123 SER cc_start: 0.7127 (p) cc_final: 0.6917 (m) REVERT: R 147 ASN cc_start: 0.8352 (p0) cc_final: 0.7957 (p0) REVERT: R 249 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7485 (tp) outliers start: 25 outliers final: 8 residues processed: 126 average time/residue: 1.4853 time to fit residues: 196.5566 Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 17 GLN B 266 HIS B 268 ASN R 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111159 restraints weight = 8576.719| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.50 r_work: 0.2917 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8268 Z= 0.104 Angle : 0.508 7.769 11244 Z= 0.264 Chirality : 0.040 0.176 1269 Planarity : 0.004 0.042 1425 Dihedral : 6.198 51.185 1331 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.36 % Allowed : 14.18 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1014 helix: 2.41 (0.26), residues: 412 sheet: 0.42 (0.34), residues: 208 loop : -0.79 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 213 HIS 0.004 0.001 HIS A 336 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR A 318 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 421) hydrogen bonds : angle 4.44081 ( 1194) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.74090 ( 6) covalent geometry : bond 0.00214 ( 8265) covalent geometry : angle 0.50810 (11238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.917 Fit side-chains REVERT: A 21 LYS cc_start: 0.8120 (mttp) cc_final: 0.7434 (tmmt) REVERT: A 195 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7664 (mttm) REVERT: A 247 GLU cc_start: 0.8591 (tt0) cc_final: 0.7742 (mm-30) REVERT: B 9 GLN cc_start: 0.7150 (mt0) cc_final: 0.6683 (tp40) REVERT: B 59 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.8097 (t80) REVERT: B 135 VAL cc_start: 0.8813 (t) cc_final: 0.8461 (p) REVERT: B 172 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: B 215 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: B 277 SER cc_start: 0.9333 (p) cc_final: 0.9082 (t) REVERT: G 47 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7435 (mt-10) REVERT: N 3 GLN cc_start: 0.8395 (mt0) cc_final: 0.7909 (mt0) REVERT: N 111 THR cc_start: 0.8650 (m) cc_final: 0.8200 (p) REVERT: N 120 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: R 198 ASP cc_start: 0.8319 (m-30) cc_final: 0.8074 (m-30) REVERT: R 249 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7487 (tp) outliers start: 20 outliers final: 4 residues processed: 127 average time/residue: 1.5290 time to fit residues: 204.0319 Evaluate side-chains 121 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 266 HIS B 268 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100603 restraints weight = 8054.283| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.50 r_work: 0.2855 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8268 Z= 0.170 Angle : 0.605 9.559 11244 Z= 0.313 Chirality : 0.043 0.185 1269 Planarity : 0.005 0.044 1425 Dihedral : 6.724 57.742 1331 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.19 % Allowed : 14.18 % Favored : 82.62 % 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: 1.26 (0.26), residues: 1014 helix: 2.39 (0.26), residues: 412 sheet: 0.44 (0.34), residues: 211 loop : -0.64 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 213 HIS 0.007 0.001 HIS B 62 PHE 0.018 0.002 PHE N 29 TYR 0.012 0.002 TYR A 318 ARG 0.011 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 421) hydrogen bonds : angle 4.64229 ( 1194) SS BOND : bond 0.00492 ( 3) SS BOND : angle 1.18019 ( 6) covalent geometry : bond 0.00381 ( 8265) covalent geometry : angle 0.60486 (11238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.938 Fit side-chains REVERT: A 21 LYS cc_start: 0.8223 (mttp) cc_final: 0.7560 (tmmt) REVERT: A 247 GLU cc_start: 0.8674 (tt0) cc_final: 0.7888 (mm-30) REVERT: B 9 GLN cc_start: 0.7331 (mt0) cc_final: 0.6405 (mm-40) REVERT: B 59 TYR cc_start: 0.9377 (OUTLIER) cc_final: 0.8266 (t80) REVERT: B 112 VAL cc_start: 0.9013 (t) cc_final: 0.8779 (m) REVERT: B 132 ASN cc_start: 0.5836 (OUTLIER) cc_final: 0.4849 (p0) REVERT: B 135 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8509 (p) REVERT: B 215 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: B 217 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8331 (pmm) REVERT: G 22 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: N 3 GLN cc_start: 0.8501 (mt0) cc_final: 0.8086 (mt0) REVERT: N 111 THR cc_start: 0.8852 (m) cc_final: 0.8396 (p) REVERT: N 120 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: R 124 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7194 (mt) REVERT: R 147 ASN cc_start: 0.8362 (p0) cc_final: 0.7953 (p0) REVERT: R 198 ASP cc_start: 0.8429 (m-30) cc_final: 0.8206 (m-30) REVERT: R 249 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7508 (tp) outliers start: 27 outliers final: 6 residues processed: 130 average time/residue: 1.5817 time to fit residues: 217.0488 Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 116 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 71 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 336 HIS B 268 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.104296 restraints weight = 8082.791| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.51 r_work: 0.2888 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8268 Z= 0.110 Angle : 0.520 8.128 11244 Z= 0.268 Chirality : 0.040 0.178 1269 Planarity : 0.004 0.044 1425 Dihedral : 6.370 58.409 1331 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.48 % Allowed : 14.89 % Favored : 82.62 % 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: 1.54 (0.27), residues: 1014 helix: 2.71 (0.26), residues: 406 sheet: 0.53 (0.35), residues: 206 loop : -0.49 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 213 HIS 0.004 0.001 HIS A 199 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR A 318 ARG 0.004 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 421) hydrogen bonds : angle 4.37484 ( 1194) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.85615 ( 6) covalent geometry : bond 0.00234 ( 8265) covalent geometry : angle 0.51945 (11238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.911 Fit side-chains REVERT: A 21 LYS cc_start: 0.8183 (mttp) cc_final: 0.7553 (tmmt) REVERT: A 247 GLU cc_start: 0.8639 (tt0) cc_final: 0.7861 (mm-30) REVERT: B 9 GLN cc_start: 0.7257 (mt0) cc_final: 0.6385 (mm-40) REVERT: B 59 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 135 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 215 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: G 17 GLU cc_start: 0.7409 (tp30) cc_final: 0.6990 (mp0) REVERT: G 22 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: N 3 GLN cc_start: 0.8471 (mt0) cc_final: 0.8027 (mt0) REVERT: N 111 THR cc_start: 0.8725 (m) cc_final: 0.8293 (p) REVERT: R 124 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7053 (mt) REVERT: R 147 ASN cc_start: 0.8236 (p0) cc_final: 0.7928 (p0) REVERT: R 198 ASP cc_start: 0.8422 (m-30) cc_final: 0.8191 (m-30) REVERT: R 249 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7498 (tp) outliers start: 21 outliers final: 2 residues processed: 125 average time/residue: 1.4879 time to fit residues: 195.6123 Evaluate side-chains 120 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 17 GLN B 268 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102381 restraints weight = 8031.170| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.50 r_work: 0.2883 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8268 Z= 0.134 Angle : 0.559 8.570 11244 Z= 0.288 Chirality : 0.041 0.182 1269 Planarity : 0.004 0.045 1425 Dihedral : 6.533 57.613 1331 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.48 % Allowed : 14.66 % Favored : 82.86 % 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: 1.56 (0.27), residues: 1014 helix: 2.69 (0.26), residues: 406 sheet: 0.56 (0.35), residues: 206 loop : -0.44 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 213 HIS 0.005 0.001 HIS B 62 PHE 0.015 0.002 PHE N 29 TYR 0.012 0.001 TYR A 318 ARG 0.011 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 421) hydrogen bonds : angle 4.44660 ( 1194) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.00324 ( 6) covalent geometry : bond 0.00295 ( 8265) covalent geometry : angle 0.55906 (11238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.820 Fit side-chains REVERT: A 21 LYS cc_start: 0.8204 (mttp) cc_final: 0.7578 (tmmt) REVERT: A 247 GLU cc_start: 0.8633 (tt0) cc_final: 0.7854 (mm-30) REVERT: A 296 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7780 (mtm110) REVERT: B 9 GLN cc_start: 0.7348 (mt0) cc_final: 0.6429 (mm-40) REVERT: B 59 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8218 (t80) REVERT: B 135 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8461 (p) REVERT: B 215 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: G 17 GLU cc_start: 0.7438 (tp30) cc_final: 0.7035 (mp0) REVERT: G 22 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: N 3 GLN cc_start: 0.8448 (mt0) cc_final: 0.8007 (mt0) REVERT: N 111 THR cc_start: 0.8782 (m) cc_final: 0.8338 (p) REVERT: R 124 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7040 (mt) REVERT: R 147 ASN cc_start: 0.8270 (p0) cc_final: 0.7849 (p0) REVERT: R 198 ASP cc_start: 0.8420 (m-30) cc_final: 0.8197 (m-30) REVERT: R 249 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7490 (tp) outliers start: 21 outliers final: 5 residues processed: 121 average time/residue: 1.4923 time to fit residues: 189.8589 Evaluate side-chains 122 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 268 ASN R 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100551 restraints weight = 8114.443| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.50 r_work: 0.2848 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8268 Z= 0.165 Angle : 0.607 9.173 11244 Z= 0.313 Chirality : 0.043 0.181 1269 Planarity : 0.005 0.045 1425 Dihedral : 6.754 57.690 1331 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.65 % Allowed : 15.60 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1014 helix: 2.65 (0.26), residues: 400 sheet: 0.45 (0.34), residues: 211 loop : -0.48 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 213 HIS 0.006 0.001 HIS B 62 PHE 0.016 0.002 PHE N 29 TYR 0.012 0.002 TYR A 318 ARG 0.013 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 421) hydrogen bonds : angle 4.61691 ( 1194) SS BOND : bond 0.00491 ( 3) SS BOND : angle 1.24613 ( 6) covalent geometry : bond 0.00371 ( 8265) covalent geometry : angle 0.60666 (11238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.960 Fit side-chains REVERT: A 21 LYS cc_start: 0.8222 (mttp) cc_final: 0.7559 (tmmt) REVERT: A 247 GLU cc_start: 0.8656 (tt0) cc_final: 0.7868 (mm-30) REVERT: B 9 GLN cc_start: 0.7447 (mt0) cc_final: 0.6492 (mm-40) REVERT: B 35 ASN cc_start: 0.7900 (t0) cc_final: 0.7328 (t0) REVERT: B 59 TYR cc_start: 0.9367 (OUTLIER) cc_final: 0.8229 (t80) REVERT: B 112 VAL cc_start: 0.8990 (t) cc_final: 0.8756 (m) REVERT: B 135 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 215 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: G 22 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: N 3 GLN cc_start: 0.8478 (mt0) cc_final: 0.8037 (mt0) REVERT: N 111 THR cc_start: 0.8879 (m) cc_final: 0.8455 (p) REVERT: R 124 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7079 (mt) REVERT: R 147 ASN cc_start: 0.8332 (p0) cc_final: 0.7887 (p0) REVERT: R 198 ASP cc_start: 0.8418 (m-30) cc_final: 0.8194 (m-30) REVERT: R 249 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7490 (tp) outliers start: 14 outliers final: 6 residues processed: 119 average time/residue: 1.8231 time to fit residues: 228.5877 Evaluate side-chains 120 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN R 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.102886 restraints weight = 8224.530| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.50 r_work: 0.2887 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8268 Z= 0.125 Angle : 0.552 8.801 11244 Z= 0.284 Chirality : 0.041 0.177 1269 Planarity : 0.004 0.045 1425 Dihedral : 6.483 57.405 1331 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.01 % Allowed : 15.13 % Favored : 82.86 % 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: 1.53 (0.27), residues: 1014 helix: 2.67 (0.26), residues: 406 sheet: 0.62 (0.35), residues: 199 loop : -0.50 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 213 HIS 0.005 0.001 HIS A 199 PHE 0.013 0.001 PHE N 29 TYR 0.012 0.001 TYR A 318 ARG 0.005 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 421) hydrogen bonds : angle 4.43531 ( 1194) SS BOND : bond 0.00224 ( 3) SS BOND : angle 0.96703 ( 6) covalent geometry : bond 0.00273 ( 8265) covalent geometry : angle 0.55176 (11238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.897 Fit side-chains REVERT: A 21 LYS cc_start: 0.8204 (mttp) cc_final: 0.7587 (tmmt) REVERT: A 247 GLU cc_start: 0.8635 (tt0) cc_final: 0.7862 (mm-30) REVERT: B 9 GLN cc_start: 0.7442 (mt0) cc_final: 0.6503 (mm-40) REVERT: B 35 ASN cc_start: 0.7890 (t0) cc_final: 0.7321 (t0) REVERT: B 59 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.8155 (t80) REVERT: B 132 ASN cc_start: 0.5814 (OUTLIER) cc_final: 0.4872 (p0) REVERT: B 135 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 215 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: G 17 GLU cc_start: 0.7424 (tp30) cc_final: 0.7034 (mp0) REVERT: G 19 LEU cc_start: 0.8560 (mt) cc_final: 0.8358 (mp) REVERT: G 22 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: N 3 GLN cc_start: 0.8451 (mt0) cc_final: 0.8010 (mt0) REVERT: N 111 THR cc_start: 0.8786 (m) cc_final: 0.8353 (p) REVERT: N 120 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: R 124 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7025 (mt) REVERT: R 147 ASN cc_start: 0.8263 (p0) cc_final: 0.7878 (p0) REVERT: R 198 ASP cc_start: 0.8366 (m-30) cc_final: 0.8132 (m-30) REVERT: R 249 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7488 (tp) outliers start: 17 outliers final: 6 residues processed: 126 average time/residue: 1.4332 time to fit residues: 189.7245 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 17 GLN B 268 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102464 restraints weight = 8075.768| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.49 r_work: 0.2881 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8268 Z= 0.132 Angle : 0.567 9.129 11244 Z= 0.291 Chirality : 0.041 0.178 1269 Planarity : 0.004 0.044 1425 Dihedral : 6.465 54.575 1331 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.89 % Allowed : 15.60 % Favored : 82.51 % 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: 1.53 (0.26), residues: 1014 helix: 2.73 (0.26), residues: 400 sheet: 0.62 (0.35), residues: 199 loop : -0.51 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 213 HIS 0.005 0.001 HIS A 336 PHE 0.015 0.002 PHE N 29 TYR 0.012 0.001 TYR A 318 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 421) hydrogen bonds : angle 4.45766 ( 1194) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.99107 ( 6) covalent geometry : bond 0.00292 ( 8265) covalent geometry : angle 0.56664 (11238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.936 Fit side-chains REVERT: A 21 LYS cc_start: 0.8201 (mttp) cc_final: 0.7578 (tmmt) REVERT: A 247 GLU cc_start: 0.8636 (tt0) cc_final: 0.7862 (mm-30) REVERT: B 9 GLN cc_start: 0.7438 (mt0) cc_final: 0.6499 (mm-40) REVERT: B 35 ASN cc_start: 0.7899 (t0) cc_final: 0.7308 (t0) REVERT: B 59 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8219 (t80) REVERT: B 132 ASN cc_start: 0.5810 (OUTLIER) cc_final: 0.4859 (p0) REVERT: B 135 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8486 (p) REVERT: B 215 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: G 17 GLU cc_start: 0.7418 (tp30) cc_final: 0.7020 (mp0) REVERT: G 19 LEU cc_start: 0.8557 (mt) cc_final: 0.8355 (mp) REVERT: G 22 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: N 3 GLN cc_start: 0.8447 (mt0) cc_final: 0.8030 (mt0) REVERT: N 111 THR cc_start: 0.8802 (m) cc_final: 0.8369 (p) REVERT: N 120 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: R 124 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7020 (mt) REVERT: R 147 ASN cc_start: 0.8258 (p0) cc_final: 0.7856 (p0) REVERT: R 198 ASP cc_start: 0.8364 (m-30) cc_final: 0.8134 (m-30) REVERT: R 249 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7452 (tp) outliers start: 16 outliers final: 6 residues processed: 120 average time/residue: 1.4695 time to fit residues: 185.0795 Evaluate side-chains 121 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 0.0040 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 17 GLN B 268 ASN R 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.143618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.103595 restraints weight = 8180.666| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.79 r_work: 0.2936 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8268 Z= 0.111 Angle : 0.536 8.489 11244 Z= 0.274 Chirality : 0.040 0.178 1269 Planarity : 0.004 0.044 1425 Dihedral : 6.230 54.385 1331 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.30 % Allowed : 16.19 % Favored : 82.51 % 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: 1.61 (0.27), residues: 1014 helix: 2.83 (0.26), residues: 400 sheet: 0.61 (0.35), residues: 199 loop : -0.49 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 213 HIS 0.004 0.001 HIS A 336 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR A 318 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 421) hydrogen bonds : angle 4.32654 ( 1194) SS BOND : bond 0.00190 ( 3) SS BOND : angle 0.81846 ( 6) covalent geometry : bond 0.00239 ( 8265) covalent geometry : angle 0.53622 (11238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7882.77 seconds wall clock time: 136 minutes 15.66 seconds (8175.66 seconds total)