Starting phenix.real_space_refine on Wed Sep 17 11:47:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0i_61055/09_2025/9j0i_61055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0i_61055/09_2025/9j0i_61055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j0i_61055/09_2025/9j0i_61055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0i_61055/09_2025/9j0i_61055.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0i_61055/09_2025/9j0i_61055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0i_61055/09_2025/9j0i_61055.cif" } resolution = 2.76 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= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 57 5.16 5 C 5473 2.51 5 N 1438 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 8529 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1613 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 12, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2487 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 6, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 83 Chain: "G" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 370 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2256 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 10, 'TRANS': 286} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "S" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1766 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'UGA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.92, per 1000 atoms: 0.23 Number of scatterers: 8529 At special positions: 0 Unit cell: (85.696, 118.976, 121.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 2 15.00 O 1559 8.00 N 1438 7.00 C 5473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 172 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " 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: 0.67 Conformation dependent library (CDL) restraints added in 374.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 40.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.621A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.351A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.654A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.517A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.160A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.548A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 23 through 48 removed outlier: 3.953A pdb=" N ALA R 35 " --> pdb=" O MET R 31 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 83 Proline residue: R 75 - end of helix removed outlier: 3.715A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 96 through 125 Processing helix chain 'R' and resid 128 through 132 Processing helix chain 'R' and resid 136 through 159 removed outlier: 4.088A pdb=" N LEU R 140 " --> pdb=" O SER R 136 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU R 148 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Proline residue: R 155 - end of helix removed outlier: 3.549A pdb=" N ILE R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 176 Processing helix chain 'R' and resid 177 through 215 removed outlier: 3.592A pdb=" N TYR R 189 " --> pdb=" O LYS R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 260 Proline residue: R 248 - end of helix removed outlier: 4.936A pdb=" N ILE R 254 " --> pdb=" O HIS R 250 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 266 through 295 removed outlier: 4.188A pdb=" N VAL R 288 " --> pdb=" O SER R 284 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N CYS R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 311 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.707A 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 removed outlier: 3.611A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.936A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.241A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.370A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.199A 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: 3.504A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.523A 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: 4.172A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.605A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.010A 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: 6.972A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.419A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.586A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.378A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1326 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: 1.60 Time building geometry restraints manager: 0.82 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: 2698 1.34 - 1.46: 1544 1.46 - 1.58: 4393 1.58 - 1.69: 4 1.69 - 1.81: 82 Bond restraints: 8721 Sorted by residual: bond pdb=" CA LYS R 77 " pdb=" C LYS R 77 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.14e+01 bond pdb=" O3A UGA R 401 " pdb=" PA UGA R 401 " ideal model delta sigma weight residual 1.652 1.595 0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" C4 UGA R 401 " pdb=" C5 UGA R 401 " ideal model delta sigma weight residual 1.442 1.387 0.055 2.00e-02 2.50e+03 7.64e+00 bond pdb=" C4 UGA R 401 " pdb=" N3 UGA R 401 " ideal model delta sigma weight residual 1.387 1.335 0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" O3B UGA R 401 " pdb=" PB UGA R 401 " ideal model delta sigma weight residual 1.646 1.598 0.048 2.00e-02 2.50e+03 5.77e+00 ... (remaining 8716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 11675 1.56 - 3.13: 161 3.13 - 4.69: 27 4.69 - 6.26: 11 6.26 - 7.82: 3 Bond angle restraints: 11877 Sorted by residual: angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 108.69 5.21 1.80e+00 3.09e-01 8.37e+00 angle pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta sigma weight residual 122.65 126.75 -4.10 1.49e+00 4.50e-01 7.57e+00 angle pdb=" O3A UGA R 401 " pdb=" PA UGA R 401 " pdb=" O5D UGA R 401 " ideal model delta sigma weight residual 93.30 101.12 -7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" C2 UGA R 401 " pdb=" N3 UGA R 401 " pdb=" C4 UGA R 401 " ideal model delta sigma weight residual 128.49 120.92 7.57 3.00e+00 1.11e-01 6.37e+00 angle pdb=" C LYS R 77 " pdb=" CA LYS R 77 " pdb=" CB LYS R 77 " ideal model delta sigma weight residual 110.88 107.27 3.61 1.57e+00 4.06e-01 5.28e+00 ... (remaining 11872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 4897 22.36 - 44.73: 184 44.73 - 67.09: 25 67.09 - 89.46: 11 89.46 - 111.82: 4 Dihedral angle restraints: 5121 sinusoidal: 1800 harmonic: 3321 Sorted by residual: dihedral pdb=" CB CYS R 94 " pdb=" SG CYS R 94 " pdb=" SG CYS R 172 " pdb=" CB CYS R 172 " ideal model delta sinusoidal sigma weight residual 93.00 164.23 -71.23 1 1.00e+01 1.00e-02 6.51e+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 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" O2' UGA R 401 " pdb=" C1' UGA R 401 " pdb=" C2' UGA R 401 " pdb=" O5' UGA R 401 " ideal model delta sinusoidal sigma weight residual 175.74 -72.44 -111.82 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1159 0.055 - 0.109: 195 0.109 - 0.164: 26 0.164 - 0.219: 1 0.219 - 0.273: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" C1D UGA R 401 " pdb=" C2D UGA R 401 " pdb=" N1 UGA R 401 " pdb=" O4D UGA R 401 " both_signs ideal model delta sigma weight residual False 2.21 2.49 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' UGA R 401 " pdb=" C1' UGA R 401 " pdb=" C3' UGA R 401 " pdb=" O2' UGA R 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C2D UGA R 401 " pdb=" C1D UGA R 401 " pdb=" C3D UGA R 401 " pdb=" O2D UGA R 401 " both_signs ideal model delta sigma weight residual False -2.62 -2.47 -0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 1379 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS R 184 " 0.014 2.00e-02 2.50e+03 1.44e-02 3.10e+00 pdb=" CG HIS R 184 " -0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS R 184 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS R 184 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS R 184 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS R 184 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " -0.019 2.00e-02 2.50e+03 1.20e-02 2.87e+00 pdb=" CG TYR S 235 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO S 236 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.019 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 141 2.68 - 3.23: 8185 3.23 - 3.79: 14279 3.79 - 4.34: 19342 4.34 - 4.90: 31917 Nonbonded interactions: 73864 Sorted by model distance: nonbonded pdb=" O TYR R 265 " pdb=" OG SER R 269 " model vdw 2.125 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR R 73 " pdb=" OG SER R 97 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.271 3.040 nonbonded pdb=" O THR R 257 " pdb=" OG1 THR R 261 " model vdw 2.283 3.040 ... (remaining 73859 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: 2.400 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.003 0.057 8723 Z= 0.153 Angle : 0.506 7.824 11881 Z= 0.266 Chirality : 0.042 0.273 1382 Planarity : 0.003 0.034 1491 Dihedral : 13.386 111.821 2971 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 1126 helix: 2.29 (0.26), residues: 416 sheet: 0.08 (0.29), residues: 292 loop : 0.31 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 98 TYR 0.026 0.001 TYR S 235 PHE 0.013 0.001 PHE B 234 TRP 0.022 0.001 TRP B 82 HIS 0.015 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8721) covalent geometry : angle 0.50616 (11877) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.46153 ( 4) hydrogen bonds : bond 0.13586 ( 475) hydrogen bonds : angle 5.50077 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.302 Fit side-chains REVERT: B 101 MET cc_start: 0.8263 (mtp) cc_final: 0.8046 (mtp) REVERT: B 260 GLU cc_start: 0.7867 (tt0) cc_final: 0.7646 (tt0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.5432 time to fit residues: 104.5191 Evaluate side-chains 121 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 259 GLN B 340 ASN R 104 ASN R 184 HIS S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124971 restraints weight = 9739.237| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.81 r_work: 0.3203 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 8723 Z= 0.247 Angle : 0.638 10.845 11881 Z= 0.339 Chirality : 0.047 0.232 1382 Planarity : 0.004 0.036 1491 Dihedral : 8.834 82.770 1274 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.32 % Allowed : 9.02 % Favored : 87.66 % 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: 1.40 (0.26), residues: 1126 helix: 2.37 (0.26), residues: 407 sheet: 0.22 (0.29), residues: 283 loop : 0.13 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.050 0.002 TYR S 235 PHE 0.021 0.002 PHE R 117 TRP 0.009 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 8721) covalent geometry : angle 0.63802 (11877) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.37579 ( 4) hydrogen bonds : bond 0.04610 ( 475) hydrogen bonds : angle 4.78405 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.331 Fit side-chains REVERT: A 14 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7499 (tm-30) REVERT: A 314 LYS cc_start: 0.7388 (ptpt) cc_final: 0.6682 (mttp) REVERT: B 101 MET cc_start: 0.8904 (mtp) cc_final: 0.8630 (mtt) REVERT: B 195 ASP cc_start: 0.8257 (p0) cc_final: 0.7944 (p0) REVERT: R 100 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7476 (mm) REVERT: S 39 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: S 192 MET cc_start: 0.8608 (ttp) cc_final: 0.8407 (ttt) outliers start: 28 outliers final: 13 residues processed: 140 average time/residue: 0.5203 time to fit residues: 77.5909 Evaluate side-chains 131 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 289 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.0570 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129954 restraints weight = 9764.519| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.86 r_work: 0.3280 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8723 Z= 0.113 Angle : 0.503 8.907 11881 Z= 0.269 Chirality : 0.042 0.293 1382 Planarity : 0.004 0.039 1491 Dihedral : 7.430 70.898 1274 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.25 % Allowed : 12.10 % Favored : 85.65 % 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: 1.34 (0.26), residues: 1126 helix: 2.25 (0.26), residues: 419 sheet: 0.23 (0.30), residues: 284 loop : 0.06 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 208 TYR 0.041 0.001 TYR S 235 PHE 0.016 0.001 PHE R 195 TRP 0.017 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8721) covalent geometry : angle 0.50313 (11877) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.44012 ( 4) hydrogen bonds : bond 0.03575 ( 475) hydrogen bonds : angle 4.44567 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.384 Fit side-chains REVERT: A 14 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7395 (tm-30) REVERT: A 21 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7642 (mtp-110) REVERT: A 314 LYS cc_start: 0.7213 (ptpt) cc_final: 0.6657 (mttp) REVERT: B 101 MET cc_start: 0.8799 (mtp) cc_final: 0.8540 (mtp) REVERT: B 195 ASP cc_start: 0.8195 (p0) cc_final: 0.7898 (p0) REVERT: R 100 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7448 (mm) REVERT: S 39 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8593 (tp40) REVERT: S 142 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8012 (mt0) outliers start: 19 outliers final: 6 residues processed: 143 average time/residue: 0.5120 time to fit residues: 78.2393 Evaluate side-chains 129 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 289 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128343 restraints weight = 9951.450| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.87 r_work: 0.3250 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8723 Z= 0.141 Angle : 0.536 9.587 11881 Z= 0.284 Chirality : 0.043 0.281 1382 Planarity : 0.004 0.041 1491 Dihedral : 6.450 68.350 1274 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.85 % Allowed : 13.64 % Favored : 83.51 % 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: 1.30 (0.26), residues: 1126 helix: 2.23 (0.26), residues: 419 sheet: 0.21 (0.30), residues: 284 loop : 0.04 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.046 0.002 TYR S 235 PHE 0.016 0.001 PHE R 195 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8721) covalent geometry : angle 0.53654 (11877) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.37155 ( 4) hydrogen bonds : bond 0.03634 ( 475) hydrogen bonds : angle 4.49456 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.349 Fit side-chains REVERT: A 14 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7416 (tm-30) REVERT: A 314 LYS cc_start: 0.7283 (ptpt) cc_final: 0.6724 (mttp) REVERT: B 101 MET cc_start: 0.8829 (mtp) cc_final: 0.8566 (mtp) REVERT: B 195 ASP cc_start: 0.8193 (p0) cc_final: 0.7888 (p0) REVERT: R 100 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7449 (mm) REVERT: R 294 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8473 (tt) REVERT: S 39 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8612 (tp40) outliers start: 24 outliers final: 11 residues processed: 138 average time/residue: 0.5119 time to fit residues: 75.5223 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 289 CYS Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** 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 = 0.3875 r_free = 0.3875 target = 0.164548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129041 restraints weight = 9815.149| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.72 r_work: 0.3279 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8723 Z= 0.123 Angle : 0.505 8.133 11881 Z= 0.271 Chirality : 0.042 0.198 1382 Planarity : 0.004 0.047 1491 Dihedral : 5.498 66.898 1274 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.85 % Allowed : 14.95 % Favored : 82.21 % 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: 1.43 (0.26), residues: 1126 helix: 2.36 (0.26), residues: 413 sheet: 0.25 (0.30), residues: 284 loop : 0.14 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.042 0.001 TYR S 235 PHE 0.015 0.001 PHE R 195 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8721) covalent geometry : angle 0.50517 (11877) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.44227 ( 4) hydrogen bonds : bond 0.03434 ( 475) hydrogen bonds : angle 4.34890 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.252 Fit side-chains REVERT: A 14 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7395 (tm-30) REVERT: A 21 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7623 (mtp-110) REVERT: A 274 PHE cc_start: 0.8565 (t80) cc_final: 0.8354 (t80) REVERT: B 101 MET cc_start: 0.8815 (mtp) cc_final: 0.8537 (mtp) REVERT: B 195 ASP cc_start: 0.8180 (p0) cc_final: 0.7898 (p0) REVERT: R 100 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7441 (mm) REVERT: S 142 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8097 (mt0) outliers start: 24 outliers final: 13 residues processed: 143 average time/residue: 0.5101 time to fit residues: 78.1232 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 289 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127176 restraints weight = 9822.575| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.71 r_work: 0.3263 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8723 Z= 0.134 Angle : 0.517 6.577 11881 Z= 0.276 Chirality : 0.042 0.187 1382 Planarity : 0.004 0.053 1491 Dihedral : 5.102 64.182 1274 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.61 % Allowed : 15.78 % Favored : 81.61 % 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: 1126 helix: 2.34 (0.26), residues: 413 sheet: 0.28 (0.30), residues: 278 loop : 0.09 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.031 0.001 TYR S 235 PHE 0.015 0.001 PHE R 195 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8721) covalent geometry : angle 0.51668 (11877) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.44829 ( 4) hydrogen bonds : bond 0.03530 ( 475) hydrogen bonds : angle 4.39828 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.259 Fit side-chains REVERT: A 14 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7389 (tm-30) REVERT: B 101 MET cc_start: 0.8821 (mtp) cc_final: 0.8551 (mtp) REVERT: B 195 ASP cc_start: 0.8164 (p0) cc_final: 0.7885 (p0) REVERT: B 217 MET cc_start: 0.8976 (pmt) cc_final: 0.8610 (pmm) REVERT: B 219 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.8266 (mmt90) REVERT: R 100 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7426 (mm) REVERT: R 294 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8425 (tt) REVERT: S 234 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7203 (tt0) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.5233 time to fit residues: 80.5574 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 289 CYS Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 84 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN R 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125621 restraints weight = 9887.347| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.75 r_work: 0.3228 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8723 Z= 0.172 Angle : 0.548 7.678 11881 Z= 0.294 Chirality : 0.043 0.209 1382 Planarity : 0.004 0.049 1491 Dihedral : 5.138 57.364 1274 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.32 % Allowed : 15.90 % Favored : 80.78 % 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: 1.32 (0.26), residues: 1126 helix: 2.29 (0.26), residues: 413 sheet: 0.17 (0.29), residues: 289 loop : 0.08 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.042 0.002 TYR S 235 PHE 0.016 0.002 PHE R 195 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8721) covalent geometry : angle 0.54791 (11877) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.32238 ( 4) hydrogen bonds : bond 0.03796 ( 475) hydrogen bonds : angle 4.51522 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.340 Fit side-chains REVERT: A 14 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7372 (tm-30) REVERT: A 21 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7570 (mtp-110) REVERT: B 101 MET cc_start: 0.8859 (mtp) cc_final: 0.8595 (mtp) REVERT: B 195 ASP cc_start: 0.8218 (p0) cc_final: 0.7930 (p0) REVERT: R 100 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7413 (mm) REVERT: R 294 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8424 (tt) REVERT: S 166 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8149 (tt) REVERT: S 234 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7626 (mt-10) outliers start: 28 outliers final: 17 residues processed: 143 average time/residue: 0.5377 time to fit residues: 82.0757 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 289 CYS Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128941 restraints weight = 9851.638| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.62 r_work: 0.3292 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8723 Z= 0.123 Angle : 0.505 5.900 11881 Z= 0.272 Chirality : 0.041 0.187 1382 Planarity : 0.004 0.048 1491 Dihedral : 4.920 54.194 1274 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.73 % Allowed : 17.44 % Favored : 79.83 % 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: 1.38 (0.26), residues: 1126 helix: 2.30 (0.26), residues: 413 sheet: 0.26 (0.30), residues: 284 loop : 0.08 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.032 0.001 TYR S 235 PHE 0.016 0.001 PHE R 195 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8721) covalent geometry : angle 0.50488 (11877) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.26427 ( 4) hydrogen bonds : bond 0.03484 ( 475) hydrogen bonds : angle 4.41128 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.378 Fit side-chains REVERT: A 14 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7409 (tm-30) REVERT: A 21 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7653 (mtp-110) REVERT: B 101 MET cc_start: 0.8819 (mtp) cc_final: 0.8546 (mtp) REVERT: B 195 ASP cc_start: 0.8162 (p0) cc_final: 0.7901 (p0) REVERT: B 217 MET cc_start: 0.8898 (pmt) cc_final: 0.8584 (pmm) REVERT: R 100 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7437 (mm) REVERT: S 234 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7542 (mt-10) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 0.5501 time to fit residues: 80.4511 Evaluate side-chains 136 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 289 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.160380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124294 restraints weight = 9856.393| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.80 r_work: 0.3207 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8723 Z= 0.200 Angle : 0.573 8.843 11881 Z= 0.306 Chirality : 0.044 0.210 1382 Planarity : 0.004 0.047 1491 Dihedral : 5.193 56.726 1274 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.37 % Allowed : 18.51 % Favored : 79.12 % 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: 1.23 (0.26), residues: 1126 helix: 2.27 (0.26), residues: 412 sheet: 0.02 (0.30), residues: 283 loop : 0.05 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.046 0.002 TYR S 235 PHE 0.017 0.002 PHE R 195 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8721) covalent geometry : angle 0.57337 (11877) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.34117 ( 4) hydrogen bonds : bond 0.03992 ( 475) hydrogen bonds : angle 4.59878 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.340 Fit side-chains REVERT: A 14 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7414 (tm-30) REVERT: B 101 MET cc_start: 0.8891 (mtp) cc_final: 0.8650 (mtt) REVERT: B 195 ASP cc_start: 0.8247 (p0) cc_final: 0.7972 (p0) REVERT: R 100 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7432 (mm) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 0.5113 time to fit residues: 75.7311 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.163782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128798 restraints weight = 9905.828| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.68 r_work: 0.3281 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8723 Z= 0.127 Angle : 0.520 7.969 11881 Z= 0.279 Chirality : 0.042 0.241 1382 Planarity : 0.004 0.045 1491 Dihedral : 4.967 56.877 1274 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.14 % Allowed : 19.10 % Favored : 78.77 % 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: 1.27 (0.26), residues: 1126 helix: 2.17 (0.26), residues: 418 sheet: 0.12 (0.30), residues: 282 loop : 0.13 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.034 0.001 TYR S 235 PHE 0.016 0.001 PHE R 195 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8721) covalent geometry : angle 0.52002 (11877) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.31069 ( 4) hydrogen bonds : bond 0.03541 ( 475) hydrogen bonds : angle 4.45366 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.372 Fit side-chains REVERT: A 14 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7530 (tm-30) REVERT: A 21 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7721 (mtp-110) REVERT: B 101 MET cc_start: 0.8830 (mtp) cc_final: 0.8563 (mtp) REVERT: B 195 ASP cc_start: 0.8208 (p0) cc_final: 0.7979 (p0) REVERT: R 100 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7480 (mm) outliers start: 18 outliers final: 13 residues processed: 137 average time/residue: 0.5049 time to fit residues: 74.0790 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 241 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122911 restraints weight = 9773.395| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.72 r_work: 0.3210 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8723 Z= 0.220 Angle : 0.595 10.081 11881 Z= 0.317 Chirality : 0.045 0.239 1382 Planarity : 0.004 0.047 1491 Dihedral : 5.284 60.101 1274 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.02 % Allowed : 19.45 % Favored : 78.53 % 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: 1.18 (0.26), residues: 1126 helix: 2.24 (0.26), residues: 411 sheet: 0.04 (0.30), residues: 285 loop : -0.03 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.049 0.002 TYR S 235 PHE 0.017 0.002 PHE R 195 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 8721) covalent geometry : angle 0.59517 (11877) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.28835 ( 4) hydrogen bonds : bond 0.04079 ( 475) hydrogen bonds : angle 4.65705 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.45 seconds wall clock time: 58 minutes 54.72 seconds (3534.72 seconds total)