Starting phenix.real_space_refine on Wed Sep 17 10:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gyo_51700/09_2025/9gyo_51700.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gyo_51700/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gyo_51700/09_2025/9gyo_51700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gyo_51700/09_2025/9gyo_51700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gyo_51700/09_2025/9gyo_51700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gyo_51700/09_2025/9gyo_51700.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.72, per 1000 atoms: 0.21 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: 0.66 Conformation dependent library (CDL) restraints added in 386.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.16 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: 1.21 Time building geometry restraints manager: 0.87 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: 2.480 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (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 ARG 0.051 0.002 ARG A 326 TYR 0.012 0.003 TYR B 85 PHE 0.014 0.003 PHE N 68 TRP 0.024 0.004 TRP B 99 HIS 0.012 0.003 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00750 ( 8265) covalent geometry : angle 1.19562 (11238) SS BOND : bond 0.24155 ( 3) SS BOND : angle 5.67578 ( 6) hydrogen bonds : bond 0.22347 ( 421) hydrogen bonds : angle 7.63210 ( 1194) *********************** 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 : 0.331 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: 0.7881 time to fit residues: 117.4806 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 : 0.251 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 266 HIS B 268 ASN B 293 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102658 restraints weight = 8175.286| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.66 r_work: 0.2916 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8268 Z= 0.164 Angle : 0.624 8.880 11244 Z= 0.328 Chirality : 0.043 0.183 1269 Planarity : 0.005 0.036 1425 Dihedral : 6.443 48.893 1334 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.25 % Allowed : 10.64 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1014 helix: 1.68 (0.24), residues: 411 sheet: 0.14 (0.33), residues: 211 loop : -1.06 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.016 0.002 TYR A 318 PHE 0.016 0.002 PHE N 29 TRP 0.016 0.002 TRP A 213 HIS 0.010 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8265) covalent geometry : angle 0.62346 (11238) SS BOND : bond 0.00587 ( 3) SS BOND : angle 1.20079 ( 6) hydrogen bonds : bond 0.05501 ( 421) hydrogen bonds : angle 4.99132 ( 1194) *********************** 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 151 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.296 Fit side-chains REVERT: A 21 LYS cc_start: 0.8186 (mttp) cc_final: 0.7507 (tmmt) REVERT: A 244 ARG cc_start: 0.8380 (mmm160) cc_final: 0.7475 (ttt-90) REVERT: A 247 GLU cc_start: 0.8586 (tt0) cc_final: 0.7834 (mm-30) REVERT: A 296 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7750 (mtm110) REVERT: A 352 ARG cc_start: 0.8396 (mmm160) cc_final: 0.8189 (tpp-160) REVERT: B 9 GLN cc_start: 0.7079 (mt0) cc_final: 0.6662 (tp40) REVERT: B 23 LYS cc_start: 0.8298 (tttp) cc_final: 0.8083 (tttp) REVERT: B 42 ARG cc_start: 0.7089 (tpt170) cc_final: 0.6782 (mmm160) REVERT: B 59 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8110 (t80) REVERT: B 96 ARG cc_start: 0.8460 (mtp180) cc_final: 0.8161 (ttp-170) REVERT: B 132 ASN cc_start: 0.5666 (OUTLIER) cc_final: 0.4927 (p0) REVERT: B 135 VAL cc_start: 0.8839 (t) cc_final: 0.8481 (p) REVERT: B 215 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: G 47 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7502 (mt-10) REVERT: N 3 GLN cc_start: 0.8504 (mt0) cc_final: 0.8070 (mt0) REVERT: N 111 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8359 (p) REVERT: N 120 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: R 198 ASP cc_start: 0.8403 (m-30) cc_final: 0.8118 (m-30) REVERT: R 249 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7653 (tp) outliers start: 19 outliers final: 4 residues processed: 141 average time/residue: 0.7039 time to fit residues: 104.0054 Evaluate side-chains 124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 128 LEU 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 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 G 59 ASN R 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106286 restraints weight = 8474.034| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.45 r_work: 0.2869 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8268 Z= 0.151 Angle : 0.584 8.949 11244 Z= 0.305 Chirality : 0.042 0.183 1269 Planarity : 0.004 0.040 1425 Dihedral : 6.623 52.407 1334 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.96 % Allowed : 12.41 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1014 helix: 2.19 (0.26), residues: 412 sheet: 0.35 (0.34), residues: 210 loop : -0.80 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.013 0.002 TYR A 318 PHE 0.017 0.002 PHE N 29 TRP 0.018 0.002 TRP A 213 HIS 0.007 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8265) covalent geometry : angle 0.58362 (11238) SS BOND : bond 0.00339 ( 3) SS BOND : angle 1.13294 ( 6) hydrogen bonds : bond 0.04734 ( 421) hydrogen bonds : angle 4.70547 ( 1194) *********************** 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 146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.278 Fit side-chains REVERT: A 21 LYS cc_start: 0.8151 (mttp) cc_final: 0.7461 (tmmt) REVERT: A 244 ARG cc_start: 0.8380 (mmm160) cc_final: 0.7364 (ttt-90) REVERT: A 247 GLU cc_start: 0.8618 (tt0) cc_final: 0.7805 (mm-30) REVERT: A 296 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7779 (mtm110) REVERT: A 352 ARG cc_start: 0.8429 (mmm160) cc_final: 0.8159 (tpp-160) REVERT: B 9 GLN cc_start: 0.7199 (mt0) cc_final: 0.6726 (tp40) REVERT: B 23 LYS cc_start: 0.8282 (tttp) cc_final: 0.8070 (tttp) REVERT: B 42 ARG cc_start: 0.7018 (tpt170) cc_final: 0.6523 (ttt90) REVERT: B 59 TYR cc_start: 0.9358 (OUTLIER) cc_final: 0.8206 (t80) REVERT: B 96 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8200 (ttp-170) REVERT: B 135 VAL cc_start: 0.8832 (t) cc_final: 0.8514 (p) REVERT: B 215 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: B 217 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8342 (pmm) REVERT: G 47 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7522 (mt-10) REVERT: N 3 GLN cc_start: 0.8417 (mt0) cc_final: 0.7980 (mt0) REVERT: N 111 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8333 (p) REVERT: N 120 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: R 147 ASN cc_start: 0.8299 (p0) cc_final: 0.7959 (p0) REVERT: R 198 ASP cc_start: 0.8366 (m-30) cc_final: 0.8108 (m-30) REVERT: R 249 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7543 (tp) outliers start: 25 outliers final: 6 residues processed: 133 average time/residue: 0.7081 time to fit residues: 98.9062 Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 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 129 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 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.146096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107892 restraints weight = 8617.433| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.63 r_work: 0.2942 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2022 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= 0.100 Angle : 0.495 7.359 11244 Z= 0.257 Chirality : 0.040 0.179 1269 Planarity : 0.004 0.043 1425 Dihedral : 6.096 51.503 1331 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.60 % Allowed : 13.48 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.26), residues: 1014 helix: 2.60 (0.26), residues: 406 sheet: 0.42 (0.34), residues: 206 loop : -0.52 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.013 0.001 TYR A 318 PHE 0.011 0.001 PHE B 199 TRP 0.017 0.001 TRP A 213 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 8265) covalent geometry : angle 0.49505 (11238) SS BOND : bond 0.00099 ( 3) SS BOND : angle 0.69615 ( 6) hydrogen bonds : bond 0.03768 ( 421) hydrogen bonds : angle 4.34991 ( 1194) *********************** 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 143 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.329 Fit side-chains REVERT: A 21 LYS cc_start: 0.8141 (mttp) cc_final: 0.7537 (tmmt) REVERT: A 247 GLU cc_start: 0.8634 (tt0) cc_final: 0.7893 (mm-30) REVERT: A 296 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7769 (mtm110) REVERT: B 9 GLN cc_start: 0.7147 (mt0) cc_final: 0.6695 (tp40) REVERT: B 42 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6549 (ttt90) REVERT: B 59 TYR cc_start: 0.9282 (OUTLIER) cc_final: 0.8147 (t80) REVERT: B 96 ARG cc_start: 0.8499 (mtp180) cc_final: 0.8199 (ttp-170) REVERT: B 135 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8471 (p) REVERT: G 17 GLU cc_start: 0.7394 (tp30) cc_final: 0.7062 (mp0) REVERT: G 47 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7399 (mt-10) REVERT: N 3 GLN cc_start: 0.8434 (mt0) cc_final: 0.8004 (mt0) REVERT: N 105 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7176 (ptt90) REVERT: N 111 THR cc_start: 0.8635 (m) cc_final: 0.8179 (p) REVERT: R 198 ASP cc_start: 0.8366 (m-30) cc_final: 0.8102 (m-30) REVERT: R 249 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7511 (tp) outliers start: 22 outliers final: 2 residues processed: 132 average time/residue: 0.6964 time to fit residues: 96.4805 Evaluate side-chains 116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 105 ARG 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 89 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 91 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.141685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102072 restraints weight = 8089.433| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.49 r_work: 0.2865 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8268 Z= 0.151 Angle : 0.580 8.867 11244 Z= 0.300 Chirality : 0.042 0.184 1269 Planarity : 0.004 0.044 1425 Dihedral : 6.582 59.126 1331 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.60 % Allowed : 14.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.26), residues: 1014 helix: 2.63 (0.26), residues: 406 sheet: 0.44 (0.34), residues: 210 loop : -0.45 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.012 0.002 TYR A 318 PHE 0.017 0.002 PHE N 29 TRP 0.015 0.002 TRP A 213 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8265) covalent geometry : angle 0.57953 (11238) SS BOND : bond 0.00444 ( 3) SS BOND : angle 1.11558 ( 6) hydrogen bonds : bond 0.04441 ( 421) hydrogen bonds : angle 4.53938 ( 1194) *********************** 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 134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.303 Fit side-chains REVERT: A 21 LYS cc_start: 0.8221 (mttp) cc_final: 0.7583 (tmmt) REVERT: A 247 GLU cc_start: 0.8671 (tt0) cc_final: 0.7896 (mm-30) REVERT: A 296 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7678 (mtm110) REVERT: B 9 GLN cc_start: 0.7263 (mt0) cc_final: 0.6434 (mm110) REVERT: B 59 TYR cc_start: 0.9365 (OUTLIER) cc_final: 0.8257 (t80) REVERT: B 96 ARG cc_start: 0.8521 (mtp180) cc_final: 0.8204 (ttp-170) REVERT: B 132 ASN cc_start: 0.5745 (OUTLIER) cc_final: 0.4790 (p0) REVERT: B 135 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8485 (p) REVERT: G 22 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: G 47 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7525 (mt-10) REVERT: N 3 GLN cc_start: 0.8505 (mt0) cc_final: 0.8076 (mt0) REVERT: N 111 THR cc_start: 0.8871 (m) cc_final: 0.8349 (p) REVERT: R 124 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7224 (mt) REVERT: R 147 ASN cc_start: 0.8254 (p0) cc_final: 0.7848 (p0) REVERT: R 198 ASP cc_start: 0.8441 (m-30) cc_final: 0.8200 (m-30) REVERT: R 249 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7498 (tp) outliers start: 22 outliers final: 6 residues processed: 127 average time/residue: 0.6834 time to fit residues: 91.0947 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 112 VAL 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 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 55 LEU 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 36 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.140565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099654 restraints weight = 8070.746| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.72 r_work: 0.2879 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8268 Z= 0.174 Angle : 0.609 9.361 11244 Z= 0.316 Chirality : 0.043 0.184 1269 Planarity : 0.005 0.045 1425 Dihedral : 6.810 58.937 1331 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.43 % Allowed : 14.30 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.26), residues: 1014 helix: 2.61 (0.26), residues: 400 sheet: 0.41 (0.34), residues: 211 loop : -0.50 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 19 TYR 0.012 0.002 TYR A 318 PHE 0.016 0.002 PHE N 29 TRP 0.017 0.002 TRP A 213 HIS 0.007 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8265) covalent geometry : angle 0.60865 (11238) SS BOND : bond 0.00501 ( 3) SS BOND : angle 1.22693 ( 6) hydrogen bonds : bond 0.04705 ( 421) hydrogen bonds : angle 4.64944 ( 1194) *********************** 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 141 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.365 Fit side-chains REVERT: A 21 LYS cc_start: 0.8183 (mttp) cc_final: 0.7516 (tmmt) REVERT: A 247 GLU cc_start: 0.8591 (tt0) cc_final: 0.7817 (mm-30) REVERT: A 296 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7681 (mtm110) REVERT: B 9 GLN cc_start: 0.7372 (mt0) cc_final: 0.6423 (mm-40) REVERT: B 35 ASN cc_start: 0.7882 (t0) cc_final: 0.7298 (t0) REVERT: B 59 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.8217 (t80) REVERT: B 96 ARG cc_start: 0.8472 (mtp180) cc_final: 0.8137 (ttp-170) REVERT: B 132 ASN cc_start: 0.5800 (OUTLIER) cc_final: 0.4857 (p0) REVERT: B 135 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8510 (p) REVERT: G 22 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: N 3 GLN cc_start: 0.8427 (mt0) cc_final: 0.8000 (mt0) REVERT: N 111 THR cc_start: 0.8912 (m) cc_final: 0.8417 (p) REVERT: N 120 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: R 124 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7199 (mt) REVERT: R 147 ASN cc_start: 0.8353 (p0) cc_final: 0.7909 (p0) REVERT: R 198 ASP cc_start: 0.8345 (m-30) cc_final: 0.8073 (m-30) REVERT: R 249 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7469 (tp) outliers start: 29 outliers final: 9 residues processed: 130 average time/residue: 0.6482 time to fit residues: 88.5422 Evaluate side-chains 126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 55 LEU 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 16 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 17 GLN 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 = 0.3590 r_free = 0.3590 target = 0.143042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103357 restraints weight = 8160.721| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.68 r_work: 0.2917 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2276 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= 0.114 Angle : 0.533 8.198 11244 Z= 0.274 Chirality : 0.040 0.176 1269 Planarity : 0.004 0.044 1425 Dihedral : 6.407 57.316 1331 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.36 % Allowed : 15.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.26), residues: 1014 helix: 2.69 (0.26), residues: 406 sheet: 0.59 (0.35), residues: 199 loop : -0.54 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 105 TYR 0.013 0.001 TYR A 318 PHE 0.012 0.001 PHE B 199 TRP 0.018 0.001 TRP A 213 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8265) covalent geometry : angle 0.53274 (11238) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.87770 ( 6) hydrogen bonds : bond 0.03947 ( 421) hydrogen bonds : angle 4.39930 ( 1194) *********************** 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 137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.406 Fit side-chains REVERT: A 21 LYS cc_start: 0.8165 (mttp) cc_final: 0.7561 (tmmt) REVERT: A 247 GLU cc_start: 0.8587 (tt0) cc_final: 0.7824 (mm-30) REVERT: A 296 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7671 (mtm110) REVERT: B 9 GLN cc_start: 0.7337 (mt0) cc_final: 0.6412 (mm-40) REVERT: B 59 TYR cc_start: 0.9302 (OUTLIER) cc_final: 0.8169 (t80) REVERT: B 96 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8142 (ttp-170) REVERT: B 135 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8457 (p) REVERT: G 17 GLU cc_start: 0.7380 (tp30) cc_final: 0.6989 (mp0) REVERT: G 22 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: N 3 GLN cc_start: 0.8405 (mt0) cc_final: 0.7992 (mt0) REVERT: N 111 THR cc_start: 0.8775 (m) cc_final: 0.8286 (p) REVERT: N 120 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: R 124 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7124 (mt) REVERT: R 147 ASN cc_start: 0.8253 (p0) cc_final: 0.7928 (p0) REVERT: R 198 ASP cc_start: 0.8362 (m-30) cc_final: 0.8091 (m-30) REVERT: R 249 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7496 (tp) outliers start: 20 outliers final: 4 residues processed: 129 average time/residue: 0.7156 time to fit residues: 97.0007 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR 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 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098211 restraints weight = 8111.281| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.56 r_work: 0.2814 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8268 Z= 0.228 Angle : 0.685 10.016 11244 Z= 0.353 Chirality : 0.046 0.188 1269 Planarity : 0.005 0.045 1425 Dihedral : 7.012 53.445 1331 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.48 % Allowed : 15.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.26), residues: 1014 helix: 2.45 (0.26), residues: 400 sheet: 0.30 (0.34), residues: 214 loop : -0.52 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 19 TYR 0.012 0.002 TYR A 318 PHE 0.017 0.002 PHE N 29 TRP 0.016 0.002 TRP A 213 HIS 0.008 0.002 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 8265) covalent geometry : angle 0.68400 (11238) SS BOND : bond 0.00658 ( 3) SS BOND : angle 1.53504 ( 6) hydrogen bonds : bond 0.05190 ( 421) hydrogen bonds : angle 4.81788 ( 1194) *********************** 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 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.273 Fit side-chains REVERT: A 21 LYS cc_start: 0.8214 (mttp) cc_final: 0.7531 (tmmt) REVERT: A 247 GLU cc_start: 0.8676 (tt0) cc_final: 0.7885 (mm-30) REVERT: A 296 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7760 (mtm110) REVERT: B 9 GLN cc_start: 0.7536 (mt0) cc_final: 0.6541 (mm-40) REVERT: B 35 ASN cc_start: 0.7864 (t0) cc_final: 0.7273 (t0) REVERT: B 59 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.8268 (t80) REVERT: B 96 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8237 (ttp-170) REVERT: B 132 ASN cc_start: 0.5758 (OUTLIER) cc_final: 0.4727 (p0) REVERT: B 135 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8521 (p) REVERT: G 17 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: G 22 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: N 3 GLN cc_start: 0.8510 (mt0) cc_final: 0.8080 (mt0) REVERT: N 111 THR cc_start: 0.9054 (m) cc_final: 0.8520 (p) REVERT: R 63 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7395 (mp) REVERT: R 124 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7178 (mt) REVERT: R 147 ASN cc_start: 0.8406 (p0) cc_final: 0.7909 (p0) REVERT: R 198 ASP cc_start: 0.8483 (m-30) cc_final: 0.8235 (m-30) REVERT: R 249 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7539 (tp) outliers start: 21 outliers final: 7 residues processed: 121 average time/residue: 0.6845 time to fit residues: 86.8396 Evaluate side-chains 120 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 63 LEU 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 59 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN 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 = 0.3532 r_free = 0.3532 target = 0.138423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098311 restraints weight = 8075.816| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.50 r_work: 0.2825 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8268 Z= 0.208 Angle : 0.662 10.403 11244 Z= 0.342 Chirality : 0.045 0.181 1269 Planarity : 0.005 0.045 1425 Dihedral : 6.913 49.644 1331 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.48 % Allowed : 15.25 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1014 helix: 2.37 (0.26), residues: 401 sheet: 0.32 (0.35), residues: 212 loop : -0.56 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 105 TYR 0.013 0.002 TYR A 318 PHE 0.017 0.002 PHE N 29 TRP 0.017 0.002 TRP A 213 HIS 0.007 0.002 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8265) covalent geometry : angle 0.66145 (11238) SS BOND : bond 0.00607 ( 3) SS BOND : angle 1.37974 ( 6) hydrogen bonds : bond 0.05012 ( 421) hydrogen bonds : angle 4.77928 ( 1194) *********************** 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 124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.311 Fit side-chains REVERT: A 21 LYS cc_start: 0.8233 (mttp) cc_final: 0.7532 (tmmt) REVERT: A 247 GLU cc_start: 0.8662 (tt0) cc_final: 0.7875 (mm-30) REVERT: A 296 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7757 (mtm110) REVERT: B 9 GLN cc_start: 0.7522 (mt0) cc_final: 0.6525 (mm-40) REVERT: B 35 ASN cc_start: 0.7877 (t0) cc_final: 0.7326 (t0) REVERT: B 59 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.8249 (t80) REVERT: B 96 ARG cc_start: 0.8594 (mtp180) cc_final: 0.8213 (ttp-170) REVERT: B 135 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8528 (p) REVERT: B 215 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: G 17 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: G 22 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: N 3 GLN cc_start: 0.8495 (mt0) cc_final: 0.8075 (mt0) REVERT: N 111 THR cc_start: 0.8980 (m) cc_final: 0.8468 (p) REVERT: R 63 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7435 (mp) REVERT: R 124 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7202 (mt) REVERT: R 147 ASN cc_start: 0.8401 (p0) cc_final: 0.7949 (p0) REVERT: R 249 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7498 (tp) outliers start: 21 outliers final: 7 residues processed: 118 average time/residue: 0.6652 time to fit residues: 82.3404 Evaluate side-chains 117 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 178 THR 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 17 GLU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 63 LEU 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 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.141214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101016 restraints weight = 8116.347| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.75 r_work: 0.2879 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8268 Z= 0.141 Angle : 0.585 9.536 11244 Z= 0.301 Chirality : 0.042 0.177 1269 Planarity : 0.004 0.044 1425 Dihedral : 6.523 49.147 1331 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.13 % Allowed : 15.72 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.26), residues: 1014 helix: 2.47 (0.26), residues: 406 sheet: 0.49 (0.35), residues: 207 loop : -0.53 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.012 0.001 TYR A 318 PHE 0.014 0.002 PHE N 29 TRP 0.020 0.002 TRP A 213 HIS 0.005 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8265) covalent geometry : angle 0.58482 (11238) SS BOND : bond 0.00319 ( 3) SS BOND : angle 1.02524 ( 6) hydrogen bonds : bond 0.04337 ( 421) hydrogen bonds : angle 4.55683 ( 1194) ********************** 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 126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.310 Fit side-chains REVERT: A 21 LYS cc_start: 0.8165 (mttp) cc_final: 0.7523 (tmmt) REVERT: A 247 GLU cc_start: 0.8599 (tt0) cc_final: 0.7806 (mm-30) REVERT: A 296 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7705 (mtm110) REVERT: B 9 GLN cc_start: 0.7415 (mt0) cc_final: 0.6439 (mm-40) REVERT: B 35 ASN cc_start: 0.7886 (t0) cc_final: 0.7322 (t0) REVERT: B 59 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8201 (t80) REVERT: B 96 ARG cc_start: 0.8543 (mtp180) cc_final: 0.8152 (ttp-170) REVERT: B 135 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8493 (p) REVERT: G 17 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: G 22 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: N 3 GLN cc_start: 0.8418 (mt0) cc_final: 0.7976 (mt0) REVERT: N 111 THR cc_start: 0.8863 (m) cc_final: 0.8350 (p) REVERT: R 63 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7377 (mp) REVERT: R 124 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7163 (mt) REVERT: R 147 ASN cc_start: 0.8330 (p0) cc_final: 0.7935 (p0) REVERT: R 198 ASP cc_start: 0.8372 (m-30) cc_final: 0.8125 (m-30) REVERT: R 249 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7469 (tp) outliers start: 18 outliers final: 8 residues processed: 121 average time/residue: 0.7050 time to fit residues: 89.4749 Evaluate side-chains 119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain R residue 63 LEU 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 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.142583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102192 restraints weight = 8110.529| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.71 r_work: 0.2915 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8268 Z= 0.122 Angle : 0.561 9.069 11244 Z= 0.287 Chirality : 0.041 0.176 1269 Planarity : 0.004 0.043 1425 Dihedral : 6.220 48.799 1331 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 16.43 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.27), residues: 1014 helix: 2.69 (0.26), residues: 400 sheet: 0.54 (0.36), residues: 202 loop : -0.54 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 286 TYR 0.012 0.001 TYR A 318 PHE 0.012 0.001 PHE N 29 TRP 0.020 0.002 TRP A 213 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8265) covalent geometry : angle 0.56091 (11238) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.89394 ( 6) hydrogen bonds : bond 0.04007 ( 421) hydrogen bonds : angle 4.42754 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.71 seconds wall clock time: 62 minutes 45.45 seconds (3765.45 seconds total)