Starting phenix.real_space_refine on Wed Feb 4 05:01:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8a_39843/02_2026/8z8a_39843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8a_39843/02_2026/8z8a_39843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z8a_39843/02_2026/8z8a_39843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8a_39843/02_2026/8z8a_39843.map" model { file = "/net/cci-nas-00/data/ceres_data/8z8a_39843/02_2026/8z8a_39843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8a_39843/02_2026/8z8a_39843.cif" } resolution = 2.82 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= 0.003 sd= 0.041 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 70 5.16 5 C 5636 2.51 5 N 1517 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8881 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2218 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 267} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 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: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'2OP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.23 Number of scatterers: 8881 At special positions: 0 Unit cell: (106.95, 117.18, 116.25, 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 70 16.00 O 1658 8.00 N 1517 7.00 C 5636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 6 " - pdb=" SG CYS R 157 " distance=1.88 Simple disulfide: pdb=" SG CYS R 7 " - pdb=" SG CYS R 252 " distance=2.19 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 165 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.58 Conformation dependent library (CDL) restraints added in 320.3 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.5% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 12 through 42 removed outlier: 3.862A pdb=" N VAL R 17 " --> pdb=" O THR R 13 " (cutoff:3.500A) Proline residue: R 19 - end of helix Processing helix chain 'R' and resid 48 through 67 removed outlier: 3.998A pdb=" N CYS R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 77 removed outlier: 3.677A pdb=" N ARG R 71 " --> pdb=" O CYS R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 118 Processing helix chain 'R' and resid 122 through 127 removed outlier: 3.544A pdb=" N ILE R 127 " --> pdb=" O VAL R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 148 Processing helix chain 'R' and resid 149 through 152 Processing helix chain 'R' and resid 167 through 171 removed outlier: 3.546A pdb=" N MET R 170 " --> pdb=" O SER R 167 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU R 171 " --> pdb=" O PHE R 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 171' Processing helix chain 'R' and resid 176 through 206 removed outlier: 3.761A pdb=" N PHE R 185 " --> pdb=" O PHE R 181 " (cutoff:3.500A) Proline residue: R 188 - end of helix Processing helix chain 'R' and resid 212 through 246 removed outlier: 3.829A pdb=" N ALA R 226 " --> pdb=" O ILE R 222 " (cutoff:3.500A) Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 246 through 251 Processing helix chain 'R' and resid 253 through 279 removed outlier: 3.836A pdb=" N SER R 265 " --> pdb=" O HIS R 261 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE R 266 " --> pdb=" O ILE R 262 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR R 267 " --> pdb=" O THR R 263 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.657A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.560A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.436A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.119A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.752A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.679A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.099A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'R' and resid 156 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 5.970A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.614A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.730A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.729A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.523A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.770A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.106A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 5.958A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.860A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.525A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1239 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: 1.57 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2081 1.33 - 1.45: 1958 1.45 - 1.57: 4931 1.57 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 9071 Sorted by residual: bond pdb=" CA 2OP R 401 " pdb=" CB 2OP R 401 " ideal model delta sigma weight residual 1.526 1.400 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" CA 2OP R 401 " pdb=" OHN 2OP R 401 " ideal model delta sigma weight residual 1.413 1.527 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" N CYS R 7 " pdb=" CA CYS R 7 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.49e+00 bond pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.44e-02 4.82e+03 7.29e+00 bond pdb=" N TYR R 149 " pdb=" CA TYR R 149 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.15e+00 ... (remaining 9066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11865 1.72 - 3.44: 342 3.44 - 5.16: 65 5.16 - 6.88: 10 6.88 - 8.60: 4 Bond angle restraints: 12286 Sorted by residual: angle pdb=" N TRP R 176 " pdb=" CA TRP R 176 " pdb=" C TRP R 176 " ideal model delta sigma weight residual 112.89 105.52 7.37 1.24e+00 6.50e-01 3.53e+01 angle pdb=" N LYS R 116 " pdb=" CA LYS R 116 " pdb=" CB LYS R 116 " ideal model delta sigma weight residual 110.28 101.68 8.60 1.55e+00 4.16e-01 3.08e+01 angle pdb=" N ASP R 12 " pdb=" CA ASP R 12 " pdb=" C ASP R 12 " ideal model delta sigma weight residual 113.18 106.99 6.19 1.33e+00 5.65e-01 2.16e+01 angle pdb=" C ARG R 8 " pdb=" N ILE R 9 " pdb=" CA ILE R 9 " ideal model delta sigma weight residual 121.65 117.50 4.15 9.40e-01 1.13e+00 1.95e+01 angle pdb=" CA ILE R 9 " pdb=" C ILE R 9 " pdb=" O ILE R 9 " ideal model delta sigma weight residual 122.63 118.92 3.71 8.70e-01 1.32e+00 1.82e+01 ... (remaining 12281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 4881 17.16 - 34.32: 409 34.32 - 51.47: 75 51.47 - 68.63: 12 68.63 - 85.79: 9 Dihedral angle restraints: 5386 sinusoidal: 2091 harmonic: 3295 Sorted by residual: dihedral pdb=" CB CYS R 7 " pdb=" SG CYS R 7 " pdb=" SG CYS R 252 " pdb=" CB CYS R 252 " ideal model delta sinusoidal sigma weight residual 93.00 17.71 75.29 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS R 6 " pdb=" SG CYS R 6 " pdb=" SG CYS R 157 " pdb=" CB CYS R 157 " ideal model delta sinusoidal sigma weight residual 93.00 159.60 -66.60 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" N ARG R 206 " pdb=" C ARG R 206 " pdb=" CA ARG R 206 " pdb=" CB ARG R 206 " ideal model delta harmonic sigma weight residual 122.80 111.46 11.34 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 5383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1103 0.057 - 0.114: 248 0.114 - 0.171: 31 0.171 - 0.228: 2 0.228 - 0.285: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CA ARG R 206 " pdb=" N ARG R 206 " pdb=" C ARG R 206 " pdb=" CB ARG R 206 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA TYR S 190 " pdb=" N TYR S 190 " pdb=" C TYR S 190 " pdb=" CB TYR S 190 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA THR R 13 " pdb=" N THR R 13 " pdb=" C THR R 13 " pdb=" CB THR R 13 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1382 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO S 75 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 346 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C ASN A 346 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 346 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 347 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 236 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.031 5.00e-02 4.00e+02 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 163 2.68 - 3.23: 8129 3.23 - 3.79: 14552 3.79 - 4.34: 20080 4.34 - 4.90: 33180 Nonbonded interactions: 76104 Sorted by model distance: nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.119 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.255 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.310 3.040 ... (remaining 76099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.310 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 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 : 0.005 0.160 9076 Z= 0.271 Angle : 0.915 61.505 12296 Z= 0.507 Chirality : 0.047 0.285 1385 Planarity : 0.005 0.074 1561 Dihedral : 13.101 85.790 3245 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.10 % Allowed : 1.35 % Favored : 98.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.06 (0.25), residues: 1123 helix: 0.81 (0.25), residues: 388 sheet: 0.09 (0.30), residues: 280 loop : -0.54 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.025 0.002 TYR S 190 PHE 0.018 0.002 PHE R 105 TRP 0.010 0.001 TRP R 81 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9071) covalent geometry : angle 0.69727 (12286) SS BOND : bond 0.09774 ( 5) SS BOND : angle 20.78464 ( 10) hydrogen bonds : bond 0.18205 ( 444) hydrogen bonds : angle 6.87640 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6793 (mt-10) REVERT: B 75 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8109 (mm110) REVERT: B 228 ASP cc_start: 0.7020 (m-30) cc_final: 0.6475 (m-30) REVERT: B 270 ILE cc_start: 0.8512 (pt) cc_final: 0.8225 (pp) REVERT: S 179 GLN cc_start: 0.8329 (tt0) cc_final: 0.8026 (tt0) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.5732 time to fit residues: 114.0004 Evaluate side-chains 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130836 restraints weight = 12718.748| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.14 r_work: 0.3322 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 0.050 9076 Z= 0.224 Angle : 0.625 11.689 12296 Z= 0.335 Chirality : 0.045 0.214 1385 Planarity : 0.005 0.071 1561 Dihedral : 4.874 30.758 1236 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.76 % Allowed : 10.27 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.55 (0.25), residues: 1123 helix: 1.61 (0.26), residues: 388 sheet: 0.22 (0.29), residues: 287 loop : -0.58 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.033 0.002 TYR S 190 PHE 0.023 0.002 PHE R 105 TRP 0.018 0.002 TRP B 169 HIS 0.006 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 9071) covalent geometry : angle 0.62254 (12286) SS BOND : bond 0.00399 ( 5) SS BOND : angle 2.06444 ( 10) hydrogen bonds : bond 0.04441 ( 444) hydrogen bonds : angle 5.04425 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.319 Fit side-chains REVERT: R 145 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7513 (tt) REVERT: R 215 MET cc_start: 0.8122 (tpt) cc_final: 0.7602 (mmt) REVERT: R 264 LEU cc_start: 0.7949 (mm) cc_final: 0.7727 (mt) REVERT: A 21 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7833 (ttm110) REVERT: A 35 LYS cc_start: 0.8410 (mppt) cc_final: 0.8170 (mptt) REVERT: A 314 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6791 (mttt) REVERT: B 197 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7850 (mmm160) REVERT: B 226 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: B 254 ASP cc_start: 0.8080 (p0) cc_final: 0.7857 (p0) REVERT: B 270 ILE cc_start: 0.8374 (pt) cc_final: 0.8088 (pp) REVERT: B 280 LYS cc_start: 0.8799 (tttm) cc_final: 0.8555 (tttm) REVERT: S 85 SER cc_start: 0.8408 (t) cc_final: 0.8192 (p) outliers start: 17 outliers final: 7 residues processed: 167 average time/residue: 0.5988 time to fit residues: 106.1870 Evaluate side-chains 160 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 294 ASN B 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.158868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129909 restraints weight = 12671.827| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.94 r_work: 0.3316 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9076 Z= 0.184 Angle : 0.567 6.056 12296 Z= 0.304 Chirality : 0.044 0.199 1385 Planarity : 0.004 0.065 1561 Dihedral : 4.695 35.661 1234 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.07 % Allowed : 12.66 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.72 (0.25), residues: 1123 helix: 1.93 (0.27), residues: 386 sheet: 0.30 (0.29), residues: 281 loop : -0.64 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.030 0.002 TYR S 190 PHE 0.017 0.002 PHE R 105 TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9071) covalent geometry : angle 0.56596 (12286) SS BOND : bond 0.00279 ( 5) SS BOND : angle 1.10845 ( 10) hydrogen bonds : bond 0.04136 ( 444) hydrogen bonds : angle 4.75987 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.257 Fit side-chains REVERT: R 16 GLN cc_start: 0.8203 (mt0) cc_final: 0.7694 (mm-40) REVERT: R 176 TRP cc_start: 0.5725 (OUTLIER) cc_final: 0.5273 (m-10) REVERT: R 180 MET cc_start: 0.7263 (ttt) cc_final: 0.6956 (mpp) REVERT: R 264 LEU cc_start: 0.8184 (mm) cc_final: 0.7955 (mt) REVERT: R 279 TYR cc_start: 0.8832 (t80) cc_final: 0.8584 (t80) REVERT: A 21 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.8006 (ttm110) REVERT: A 29 LYS cc_start: 0.8254 (tppt) cc_final: 0.7936 (tppt) REVERT: A 275 GLU cc_start: 0.7872 (tt0) cc_final: 0.7623 (tm-30) REVERT: B 61 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8264 (tmm) REVERT: B 197 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7979 (mmm160) REVERT: B 254 ASP cc_start: 0.8275 (p0) cc_final: 0.8056 (p0) REVERT: B 270 ILE cc_start: 0.8358 (pt) cc_final: 0.8079 (pp) outliers start: 20 outliers final: 7 residues processed: 162 average time/residue: 0.5730 time to fit residues: 98.3945 Evaluate side-chains 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 176 TRP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.0570 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 GLN A 269 ASN B 62 HIS S 167 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128082 restraints weight = 12765.484| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.13 r_work: 0.3287 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9076 Z= 0.213 Angle : 0.578 7.184 12296 Z= 0.310 Chirality : 0.045 0.216 1385 Planarity : 0.005 0.063 1561 Dihedral : 4.702 32.697 1234 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.18 % Allowed : 13.90 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.66 (0.25), residues: 1123 helix: 1.90 (0.27), residues: 387 sheet: 0.26 (0.28), residues: 280 loop : -0.70 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.033 0.002 TYR S 190 PHE 0.020 0.002 PHE R 105 TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9071) covalent geometry : angle 0.57757 (12286) SS BOND : bond 0.00349 ( 5) SS BOND : angle 0.96496 ( 10) hydrogen bonds : bond 0.04145 ( 444) hydrogen bonds : angle 4.74046 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.343 Fit side-chains REVERT: R 42 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: R 176 TRP cc_start: 0.5570 (OUTLIER) cc_final: 0.5248 (m-10) REVERT: A 21 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7741 (ttm110) REVERT: A 29 LYS cc_start: 0.8251 (tppt) cc_final: 0.7895 (mppt) REVERT: A 275 GLU cc_start: 0.7822 (tt0) cc_final: 0.7583 (tm-30) REVERT: B 156 GLN cc_start: 0.8398 (mt0) cc_final: 0.8087 (mt0) REVERT: B 197 ARG cc_start: 0.8276 (tpp80) cc_final: 0.7898 (mmm160) REVERT: B 226 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: B 254 ASP cc_start: 0.8064 (p0) cc_final: 0.7814 (p0) REVERT: B 270 ILE cc_start: 0.8369 (pt) cc_final: 0.8088 (pp) outliers start: 21 outliers final: 11 residues processed: 151 average time/residue: 0.5417 time to fit residues: 86.9420 Evaluate side-chains 149 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 PHE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 176 TRP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 94 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 GLN A 269 ASN B 62 HIS B 340 ASN S 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.156103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127245 restraints weight = 12517.389| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.13 r_work: 0.3285 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9076 Z= 0.273 Angle : 0.639 7.641 12296 Z= 0.338 Chirality : 0.047 0.229 1385 Planarity : 0.005 0.064 1561 Dihedral : 4.964 46.942 1234 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.90 % Allowed : 13.80 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.49 (0.25), residues: 1123 helix: 1.70 (0.27), residues: 386 sheet: 0.19 (0.29), residues: 279 loop : -0.74 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 240 TYR 0.035 0.002 TYR S 190 PHE 0.020 0.002 PHE R 105 TRP 0.040 0.003 TRP R 176 HIS 0.006 0.002 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 9071) covalent geometry : angle 0.63838 (12286) SS BOND : bond 0.00404 ( 5) SS BOND : angle 1.04158 ( 10) hydrogen bonds : bond 0.04485 ( 444) hydrogen bonds : angle 4.84938 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: R 42 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: A 21 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7756 (ttm110) REVERT: B 155 ASN cc_start: 0.8450 (t0) cc_final: 0.7946 (t0) REVERT: B 156 GLN cc_start: 0.8414 (mt0) cc_final: 0.8156 (mt0) REVERT: B 197 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7902 (mmm160) REVERT: B 219 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7317 (mmt180) REVERT: B 226 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: B 254 ASP cc_start: 0.8063 (p0) cc_final: 0.7801 (p0) REVERT: S 234 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7837 (pm20) outliers start: 28 outliers final: 14 residues processed: 149 average time/residue: 0.5667 time to fit residues: 89.4763 Evaluate side-chains 153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 PHE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 GLN R 207 GLN R 212 GLN A 244 HIS B 62 HIS B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128617 restraints weight = 12495.140| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.17 r_work: 0.3308 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9076 Z= 0.168 Angle : 0.541 8.406 12296 Z= 0.290 Chirality : 0.043 0.198 1385 Planarity : 0.004 0.063 1561 Dihedral : 4.693 43.664 1234 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.70 % Allowed : 15.56 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.74 (0.25), residues: 1123 helix: 2.10 (0.27), residues: 381 sheet: 0.13 (0.28), residues: 283 loop : -0.60 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 130 TYR 0.030 0.002 TYR S 190 PHE 0.015 0.002 PHE R 105 TRP 0.032 0.002 TRP R 176 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9071) covalent geometry : angle 0.54061 (12286) SS BOND : bond 0.00352 ( 5) SS BOND : angle 0.81386 ( 10) hydrogen bonds : bond 0.03834 ( 444) hydrogen bonds : angle 4.67478 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.333 Fit side-chains REVERT: R 145 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7167 (mt) REVERT: R 225 VAL cc_start: 0.8696 (t) cc_final: 0.8377 (m) REVERT: R 260 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6831 (tt) REVERT: A 21 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7711 (ttm110) REVERT: A 29 LYS cc_start: 0.8256 (tppt) cc_final: 0.7967 (tppt) REVERT: A 53 MET cc_start: 0.7040 (mmt) cc_final: 0.6714 (mmm) REVERT: B 156 GLN cc_start: 0.8382 (mt0) cc_final: 0.8132 (mt0) REVERT: B 197 ARG cc_start: 0.8284 (tpp80) cc_final: 0.7911 (mmm160) REVERT: B 217 MET cc_start: 0.8298 (pmm) cc_final: 0.7767 (ppp) REVERT: B 219 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7236 (mmt180) REVERT: B 254 ASP cc_start: 0.8017 (p0) cc_final: 0.7725 (p0) REVERT: B 280 LYS cc_start: 0.8784 (tttm) cc_final: 0.8427 (tttp) REVERT: S 87 ARG cc_start: 0.7050 (ptp90) cc_final: 0.6498 (ptp-110) REVERT: S 234 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7786 (pm20) outliers start: 26 outliers final: 14 residues processed: 157 average time/residue: 0.5694 time to fit residues: 94.5246 Evaluate side-chains 158 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.0060 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 107 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 GLN R 212 GLN A 244 HIS A 304 GLN B 62 HIS B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.158338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130947 restraints weight = 12715.691| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.81 r_work: 0.3372 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9076 Z= 0.114 Angle : 0.496 7.494 12296 Z= 0.267 Chirality : 0.041 0.176 1385 Planarity : 0.004 0.062 1561 Dihedral : 4.439 43.038 1234 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.59 % Allowed : 16.18 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.92 (0.25), residues: 1123 helix: 2.32 (0.27), residues: 384 sheet: 0.09 (0.28), residues: 283 loop : -0.50 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 130 TYR 0.026 0.001 TYR S 190 PHE 0.012 0.001 PHE R 197 TRP 0.029 0.002 TRP R 176 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9071) covalent geometry : angle 0.49564 (12286) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.99328 ( 10) hydrogen bonds : bond 0.03412 ( 444) hydrogen bonds : angle 4.49882 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.216 Fit side-chains REVERT: R 97 MET cc_start: 0.8328 (ttm) cc_final: 0.8109 (tpp) REVERT: R 225 VAL cc_start: 0.8740 (t) cc_final: 0.8432 (m) REVERT: A 21 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7870 (ttm110) REVERT: A 28 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7329 (mm-30) REVERT: A 29 LYS cc_start: 0.8339 (tppt) cc_final: 0.8018 (tppt) REVERT: B 134 ARG cc_start: 0.8116 (ptm-80) cc_final: 0.7859 (ptp90) REVERT: B 156 GLN cc_start: 0.8495 (mt0) cc_final: 0.8270 (mt0) REVERT: B 197 ARG cc_start: 0.8408 (tpp80) cc_final: 0.7959 (mmm160) REVERT: B 217 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7840 (ppp) REVERT: B 226 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: B 254 ASP cc_start: 0.8185 (p0) cc_final: 0.7890 (p0) REVERT: B 262 MET cc_start: 0.8128 (mtm) cc_final: 0.7716 (ttm) REVERT: S 87 ARG cc_start: 0.7098 (ptp90) cc_final: 0.6521 (ptp-110) REVERT: S 178 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8574 (tp) REVERT: S 194 ASN cc_start: 0.8948 (m110) cc_final: 0.8706 (m110) REVERT: S 234 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7904 (pm20) outliers start: 25 outliers final: 13 residues processed: 169 average time/residue: 0.5181 time to fit residues: 92.8926 Evaluate side-chains 171 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 GLN A 244 HIS B 62 HIS B 75 GLN B 259 GLN G 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.158140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130965 restraints weight = 12574.978| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.00 r_work: 0.3315 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9076 Z= 0.175 Angle : 0.546 8.127 12296 Z= 0.293 Chirality : 0.043 0.205 1385 Planarity : 0.004 0.063 1561 Dihedral : 4.574 43.413 1234 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.49 % Allowed : 16.18 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.86 (0.25), residues: 1123 helix: 2.20 (0.26), residues: 386 sheet: 0.16 (0.29), residues: 277 loop : -0.55 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.032 0.002 TYR S 190 PHE 0.018 0.002 PHE R 105 TRP 0.029 0.002 TRP B 339 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9071) covalent geometry : angle 0.54556 (12286) SS BOND : bond 0.00305 ( 5) SS BOND : angle 1.06940 ( 10) hydrogen bonds : bond 0.03795 ( 444) hydrogen bonds : angle 4.59638 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.408 Fit side-chains REVERT: R 225 VAL cc_start: 0.8698 (t) cc_final: 0.8374 (m) REVERT: R 260 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6853 (tt) REVERT: A 29 LYS cc_start: 0.8308 (tppt) cc_final: 0.8011 (tppt) REVERT: B 46 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: B 156 GLN cc_start: 0.8396 (mt0) cc_final: 0.8187 (mt0) REVERT: B 197 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7807 (mmm160) REVERT: B 217 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7847 (ppp) REVERT: B 226 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: B 254 ASP cc_start: 0.8053 (p0) cc_final: 0.7746 (p0) REVERT: S 87 ARG cc_start: 0.7097 (ptp90) cc_final: 0.6598 (ptp-110) REVERT: S 178 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8475 (tp) REVERT: S 234 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7810 (pm20) outliers start: 24 outliers final: 14 residues processed: 160 average time/residue: 0.5689 time to fit residues: 96.2621 Evaluate side-chains 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 GLN R 207 GLN A 244 HIS A 304 GLN B 62 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.157903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130536 restraints weight = 12568.304| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.01 r_work: 0.3340 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9076 Z= 0.147 Angle : 0.528 8.332 12296 Z= 0.284 Chirality : 0.042 0.190 1385 Planarity : 0.004 0.063 1561 Dihedral : 4.548 42.428 1234 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.28 % Allowed : 16.80 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.92 (0.25), residues: 1123 helix: 2.25 (0.27), residues: 387 sheet: 0.23 (0.29), residues: 275 loop : -0.53 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.029 0.001 TYR S 190 PHE 0.015 0.001 PHE R 197 TRP 0.030 0.002 TRP B 339 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9071) covalent geometry : angle 0.52753 (12286) SS BOND : bond 0.00273 ( 5) SS BOND : angle 0.87239 ( 10) hydrogen bonds : bond 0.03628 ( 444) hydrogen bonds : angle 4.55135 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.294 Fit side-chains REVERT: R 225 VAL cc_start: 0.8741 (t) cc_final: 0.8427 (m) REVERT: R 260 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6969 (tt) REVERT: A 21 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7871 (ttm-80) REVERT: A 28 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7390 (mm-30) REVERT: A 29 LYS cc_start: 0.8353 (tppt) cc_final: 0.8017 (tppt) REVERT: B 197 ARG cc_start: 0.8317 (tpp80) cc_final: 0.7892 (mmm160) REVERT: B 217 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7738 (ppp) REVERT: B 219 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7193 (mmt180) REVERT: B 226 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: B 254 ASP cc_start: 0.8231 (p0) cc_final: 0.7895 (p0) REVERT: B 262 MET cc_start: 0.8161 (mtm) cc_final: 0.7824 (ttm) REVERT: S 87 ARG cc_start: 0.7142 (ptp90) cc_final: 0.6616 (ptp-110) REVERT: S 178 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8578 (tp) REVERT: S 234 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7915 (pm20) outliers start: 22 outliers final: 15 residues processed: 154 average time/residue: 0.5702 time to fit residues: 92.8407 Evaluate side-chains 162 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 207 GLN A 244 HIS B 62 HIS B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129562 restraints weight = 12469.850| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.99 r_work: 0.3302 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9076 Z= 0.203 Angle : 0.584 8.598 12296 Z= 0.311 Chirality : 0.045 0.254 1385 Planarity : 0.004 0.063 1561 Dihedral : 4.687 43.160 1234 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.28 % Allowed : 16.91 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.85 (0.25), residues: 1123 helix: 2.13 (0.26), residues: 386 sheet: 0.22 (0.29), residues: 277 loop : -0.54 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.033 0.002 TYR S 190 PHE 0.020 0.002 PHE R 105 TRP 0.037 0.002 TRP B 339 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9071) covalent geometry : angle 0.58384 (12286) SS BOND : bond 0.00341 ( 5) SS BOND : angle 0.97613 ( 10) hydrogen bonds : bond 0.03977 ( 444) hydrogen bonds : angle 4.66583 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.211 Fit side-chains REVERT: R 225 VAL cc_start: 0.8710 (t) cc_final: 0.8389 (m) REVERT: R 260 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6920 (tt) REVERT: A 29 LYS cc_start: 0.8296 (tppt) cc_final: 0.8008 (tppt) REVERT: B 197 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7831 (mmm160) REVERT: B 217 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7658 (ppp) REVERT: B 219 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7194 (mmt180) REVERT: B 226 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: B 254 ASP cc_start: 0.8047 (p0) cc_final: 0.7737 (p0) REVERT: G 47 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: S 87 ARG cc_start: 0.7063 (ptp90) cc_final: 0.6563 (ptp-110) REVERT: S 178 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8481 (tp) REVERT: S 234 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7789 (pm20) outliers start: 22 outliers final: 13 residues processed: 152 average time/residue: 0.5964 time to fit residues: 95.7938 Evaluate side-chains 162 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 89 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 GLN R 207 GLN A 244 HIS B 62 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.159023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131617 restraints weight = 12434.475| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.57 r_work: 0.3398 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9076 Z= 0.114 Angle : 0.504 9.331 12296 Z= 0.272 Chirality : 0.041 0.172 1385 Planarity : 0.004 0.062 1561 Dihedral : 4.442 40.373 1234 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.87 % Allowed : 17.32 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.99 (0.25), residues: 1123 helix: 2.33 (0.27), residues: 388 sheet: 0.17 (0.29), residues: 278 loop : -0.46 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.026 0.001 TYR S 190 PHE 0.014 0.001 PHE R 197 TRP 0.026 0.002 TRP R 176 HIS 0.004 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9071) covalent geometry : angle 0.50414 (12286) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.70036 ( 10) hydrogen bonds : bond 0.03366 ( 444) hydrogen bonds : angle 4.48693 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3371.35 seconds wall clock time: 58 minutes 4.09 seconds (3484.09 seconds total)