Starting phenix.real_space_refine on Sun Aug 24 02:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zr5_60392/08_2025/8zr5_60392_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zr5_60392/08_2025/8zr5_60392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zr5_60392/08_2025/8zr5_60392_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zr5_60392/08_2025/8zr5_60392_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zr5_60392/08_2025/8zr5_60392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zr5_60392/08_2025/8zr5_60392.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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: 6 Type Number sf(0) Gaussians S 55 5.16 5 C 5171 2.51 5 N 1417 2.21 5 O 1508 1.98 5 F 1 1.80 5 H 8043 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16195 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3903 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5098 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1910 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "C" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4365 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1D8M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.17 Number of scatterers: 16195 At special positions: 0 Unit cell: (82.45, 102.85, 134.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 F 1 9.00 O 1508 8.00 N 1417 7.00 C 5171 6.00 H 8043 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 155 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 323.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 44.2% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.890A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.616A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.626A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.551A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.032A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.185A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.724A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.615A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.620A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.944A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.560A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'C' and resid 7 through 36 removed outlier: 3.552A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 66 removed outlier: 3.960A pdb=" N CYS C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 109 removed outlier: 3.851A pdb=" N LEU C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 101 " --> pdb=" O MET C 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 118 through 138 removed outlier: 3.938A pdb=" N GLY C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.526A pdb=" N VAL C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 removed outlier: 3.979A pdb=" N VAL C 166 " --> pdb=" O HIS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 210 removed outlier: 3.514A pdb=" N LEU C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 190 " --> pdb=" O CYS C 186 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.624A pdb=" N SER C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.901A pdb=" N PHE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 265 removed outlier: 4.195A pdb=" N LEU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.619A pdb=" N VAL C 269 " --> pdb=" O TRP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 283 through 298 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.294A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.804A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.743A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.977A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.558A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.567A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.131A 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: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.636A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.042A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 1856 1.05 - 1.24: 7281 1.24 - 1.43: 2437 1.43 - 1.62: 4704 1.62 - 1.81: 79 Bond restraints: 16357 Sorted by residual: bond pdb=" CE2 PHE C 165 " pdb=" HE2 PHE C 165 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" CZ PHE A 238 " pdb=" HZ PHE A 238 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" CZ2 TRP A 234 " pdb=" HZ2 TRP A 234 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" CZ PHE C 161 " pdb=" HZ PHE C 161 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" CD2 HIS C 195 " pdb=" HD2 HIS C 195 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.27e+01 ... (remaining 16352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 28718 1.90 - 3.79: 639 3.79 - 5.69: 61 5.69 - 7.58: 8 7.58 - 9.48: 5 Bond angle restraints: 29431 Sorted by residual: angle pdb=" CB HIS C 34 " pdb=" CG HIS C 34 " pdb=" CD2 HIS C 34 " ideal model delta sigma weight residual 131.20 122.61 8.59 1.30e+00 5.92e-01 4.37e+01 angle pdb=" CB HIS C 34 " pdb=" CG HIS C 34 " pdb=" ND1 HIS C 34 " ideal model delta sigma weight residual 122.70 131.27 -8.57 1.50e+00 4.44e-01 3.26e+01 angle pdb=" C ILE C 143 " pdb=" N PRO C 144 " pdb=" CA PRO C 144 " ideal model delta sigma weight residual 120.47 114.57 5.90 1.07e+00 8.73e-01 3.04e+01 angle pdb=" N SER B 84 " pdb=" CA SER B 84 " pdb=" C SER B 84 " ideal model delta sigma weight residual 111.33 117.09 -5.76 1.21e+00 6.83e-01 2.27e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.80 120.28 -9.48 2.13e+00 2.20e-01 1.98e+01 ... (remaining 29426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6752 17.65 - 35.31: 676 35.31 - 52.96: 220 52.96 - 70.62: 55 70.62 - 88.27: 15 Dihedral angle restraints: 7718 sinusoidal: 4147 harmonic: 3571 Sorted by residual: dihedral pdb=" CB CYS C 78 " pdb=" SG CYS C 78 " pdb=" SG CYS C 155 " pdb=" CB CYS C 155 " ideal model delta sinusoidal sigma weight residual 93.00 161.84 -68.84 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB GLU C 261 " pdb=" CG GLU C 261 " pdb=" CD GLU C 261 " pdb=" OE1 GLU C 261 " ideal model delta sinusoidal sigma weight residual 0.00 -87.37 87.37 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 7715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 995 0.045 - 0.090: 210 0.090 - 0.135: 67 0.135 - 0.180: 4 0.180 - 0.224: 5 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA LEU C 258 " pdb=" N LEU C 258 " pdb=" C LEU C 258 " pdb=" CB LEU C 258 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 143 " pdb=" N ILE C 143 " pdb=" C ILE C 143 " pdb=" CB ILE C 143 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1278 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 237 " 0.327 2.00e-02 2.50e+03 4.22e-01 2.67e+03 pdb=" CG ASN B 237 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 237 " -0.317 2.00e-02 2.50e+03 pdb=" ND2 ASN B 237 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 237 " 0.666 2.00e-02 2.50e+03 pdb="HD22 ASN B 237 " -0.645 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 283 " 0.273 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CD GLN C 283 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN C 283 " -0.260 2.00e-02 2.50e+03 pdb=" NE2 GLN C 283 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN C 283 " -0.401 2.00e-02 2.50e+03 pdb="HE22 GLN C 283 " 0.409 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 154 " 0.226 2.00e-02 2.50e+03 2.25e-01 7.57e+02 pdb=" CD GLN C 154 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN C 154 " -0.212 2.00e-02 2.50e+03 pdb=" NE2 GLN C 154 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 154 " 0.327 2.00e-02 2.50e+03 pdb="HE22 GLN C 154 " -0.315 2.00e-02 2.50e+03 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 194 1.94 - 2.60: 16681 2.60 - 3.27: 47196 3.27 - 3.93: 60747 3.93 - 4.60: 93046 Nonbonded interactions: 217864 Sorted by model distance: nonbonded pdb=" HG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 1.272 2.450 nonbonded pdb=" O VAL C 56 " pdb=" HG SER C 59 " model vdw 1.290 2.450 nonbonded pdb=" OD1 ASP C 51 " pdb=" HG SER C 92 " model vdw 1.309 2.450 nonbonded pdb=" O THR B 86 " pdb=" HG1 THR B 87 " model vdw 1.338 2.450 nonbonded pdb=" O ASP B 195 " pdb=" HG1 THR B 196 " model vdw 1.355 2.450 ... (remaining 217859 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: 5.930 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: 0.050 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.730 Find NCS groups from input model: 0.040 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 0.100 8316 Z= 0.329 Angle : 0.711 9.477 11267 Z= 0.438 Chirality : 0.043 0.224 1281 Planarity : 0.005 0.051 1435 Dihedral : 15.902 88.273 2999 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.23 % Allowed : 17.24 % Favored : 82.53 % 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: -0.42 (0.26), residues: 1028 helix: 0.34 (0.27), residues: 414 sheet: 0.04 (0.35), residues: 200 loop : -0.98 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.016 0.001 TYR C 134 PHE 0.011 0.001 PHE C 158 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 8314) covalent geometry : angle 0.71045 (11263) SS BOND : bond 0.00616 ( 2) SS BOND : angle 1.34070 ( 4) hydrogen bonds : bond 0.15315 ( 409) hydrogen bonds : angle 6.76096 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 ASP cc_start: 0.7030 (t70) cc_final: 0.6827 (m-30) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.1897 time to fit residues: 31.9493 Evaluate side-chains 113 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107598 restraints weight = 27312.346| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.37 r_work: 0.3017 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8316 Z= 0.141 Angle : 0.514 5.818 11267 Z= 0.281 Chirality : 0.040 0.143 1281 Planarity : 0.004 0.051 1435 Dihedral : 4.592 54.999 1158 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.26 % Allowed : 17.24 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.27), residues: 1028 helix: 1.20 (0.27), residues: 417 sheet: -0.12 (0.35), residues: 199 loop : -1.08 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 81 TYR 0.016 0.001 TYR C 281 PHE 0.012 0.001 PHE B 151 TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8314) covalent geometry : angle 0.51402 (11263) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.48502 ( 4) hydrogen bonds : bond 0.05278 ( 409) hydrogen bonds : angle 4.78760 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASP cc_start: 0.8245 (m-30) cc_final: 0.7821 (m-30) REVERT: B 170 ASP cc_start: 0.8436 (t0) cc_final: 0.7678 (p0) REVERT: C 37 ASP cc_start: 0.7190 (t70) cc_final: 0.6872 (m-30) outliers start: 11 outliers final: 7 residues processed: 126 average time/residue: 0.1839 time to fit residues: 31.0767 Evaluate side-chains 119 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106554 restraints weight = 27610.068| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.39 r_work: 0.3093 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8316 Z= 0.141 Angle : 0.491 5.737 11267 Z= 0.266 Chirality : 0.040 0.144 1281 Planarity : 0.003 0.050 1435 Dihedral : 4.059 18.737 1156 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.92 % Allowed : 18.74 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.27), residues: 1028 helix: 1.66 (0.28), residues: 416 sheet: -0.06 (0.35), residues: 197 loop : -1.09 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 81 TYR 0.014 0.001 TYR A 37 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8314) covalent geometry : angle 0.49095 (11263) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.54836 ( 4) hydrogen bonds : bond 0.04802 ( 409) hydrogen bonds : angle 4.51847 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASP cc_start: 0.8188 (m-30) cc_final: 0.7785 (m-30) REVERT: B 170 ASP cc_start: 0.8477 (t0) cc_final: 0.7745 (p0) REVERT: C 37 ASP cc_start: 0.7142 (t70) cc_final: 0.6818 (m-30) outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.2037 time to fit residues: 32.9960 Evaluate side-chains 117 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105841 restraints weight = 27358.204| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.37 r_work: 0.3068 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8316 Z= 0.139 Angle : 0.483 5.865 11267 Z= 0.262 Chirality : 0.039 0.143 1281 Planarity : 0.003 0.049 1435 Dihedral : 4.026 19.398 1156 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.61 % Allowed : 18.05 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.27), residues: 1028 helix: 1.82 (0.28), residues: 418 sheet: -0.03 (0.36), residues: 197 loop : -1.03 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.014 0.001 TYR A 37 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8314) covalent geometry : angle 0.48330 (11263) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.42674 ( 4) hydrogen bonds : bond 0.04603 ( 409) hydrogen bonds : angle 4.38077 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8492 (t0) cc_final: 0.7749 (p0) REVERT: C 37 ASP cc_start: 0.7218 (t70) cc_final: 0.6844 (m-30) REVERT: C 105 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8424 (mp) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.2054 time to fit residues: 34.0705 Evaluate side-chains 118 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 66 optimal weight: 0.4980 chunk 65 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108124 restraints weight = 27185.411| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.37 r_work: 0.3118 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8316 Z= 0.096 Angle : 0.452 4.902 11267 Z= 0.241 Chirality : 0.038 0.146 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.815 17.811 1156 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.26 % Allowed : 18.05 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.27), residues: 1028 helix: 2.13 (0.28), residues: 412 sheet: 0.11 (0.36), residues: 195 loop : -0.96 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 62 TYR 0.010 0.001 TYR A 37 PHE 0.010 0.001 PHE B 199 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8314) covalent geometry : angle 0.45241 (11263) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.37599 ( 4) hydrogen bonds : bond 0.03972 ( 409) hydrogen bonds : angle 4.17750 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8438 (t0) cc_final: 0.7860 (p0) REVERT: C 37 ASP cc_start: 0.7051 (t70) cc_final: 0.6757 (m-30) REVERT: C 105 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8421 (mp) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 0.1984 time to fit residues: 32.5745 Evaluate side-chains 115 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107958 restraints weight = 27185.927| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.37 r_work: 0.3127 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8316 Z= 0.101 Angle : 0.450 5.010 11267 Z= 0.240 Chirality : 0.038 0.143 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.769 18.609 1156 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.38 % Allowed : 17.70 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.27), residues: 1028 helix: 2.36 (0.28), residues: 405 sheet: 0.14 (0.36), residues: 196 loop : -0.93 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 62 TYR 0.011 0.001 TYR A 37 PHE 0.011 0.001 PHE B 199 TRP 0.009 0.001 TRP A 234 HIS 0.002 0.000 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8314) covalent geometry : angle 0.44956 (11263) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.35958 ( 4) hydrogen bonds : bond 0.03900 ( 409) hydrogen bonds : angle 4.09678 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8414 (t0) cc_final: 0.7884 (p0) REVERT: G 22 GLU cc_start: 0.7391 (tt0) cc_final: 0.6541 (mt-10) REVERT: C 37 ASP cc_start: 0.7137 (t70) cc_final: 0.6773 (m-30) REVERT: C 105 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8432 (mp) outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.2088 time to fit residues: 34.1827 Evaluate side-chains 119 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106322 restraints weight = 27148.846| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.37 r_work: 0.3101 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8316 Z= 0.132 Angle : 0.471 5.698 11267 Z= 0.252 Chirality : 0.039 0.142 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.907 19.914 1156 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.84 % Allowed : 17.70 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.27), residues: 1028 helix: 2.14 (0.28), residues: 412 sheet: 0.06 (0.37), residues: 199 loop : -1.01 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 68 TYR 0.014 0.001 TYR A 37 PHE 0.012 0.001 PHE B 199 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8314) covalent geometry : angle 0.47119 (11263) SS BOND : bond 0.00215 ( 2) SS BOND : angle 0.43346 ( 4) hydrogen bonds : bond 0.04244 ( 409) hydrogen bonds : angle 4.15656 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8418 (t0) cc_final: 0.7810 (p0) REVERT: B 215 GLU cc_start: 0.7593 (tt0) cc_final: 0.7324 (tt0) REVERT: G 21 MET cc_start: 0.7452 (ttp) cc_final: 0.7131 (ttp) REVERT: G 22 GLU cc_start: 0.7395 (tt0) cc_final: 0.6580 (mt-10) REVERT: C 37 ASP cc_start: 0.7140 (t70) cc_final: 0.6753 (m-30) REVERT: C 105 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8452 (mp) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.2005 time to fit residues: 32.8846 Evaluate side-chains 122 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107265 restraints weight = 27208.815| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.31 r_work: 0.3029 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8316 Z= 0.145 Angle : 0.482 5.944 11267 Z= 0.259 Chirality : 0.039 0.144 1281 Planarity : 0.003 0.049 1435 Dihedral : 4.036 20.954 1156 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.72 % Allowed : 17.47 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.27), residues: 1028 helix: 2.08 (0.27), residues: 412 sheet: -0.01 (0.36), residues: 204 loop : -1.01 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.014 0.001 TYR A 37 PHE 0.013 0.001 PHE B 199 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8314) covalent geometry : angle 0.48195 (11263) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.41903 ( 4) hydrogen bonds : bond 0.04433 ( 409) hydrogen bonds : angle 4.19984 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8463 (t0) cc_final: 0.7784 (p0) REVERT: G 14 LYS cc_start: 0.7232 (tptt) cc_final: 0.6664 (mtmt) REVERT: G 22 GLU cc_start: 0.7313 (tt0) cc_final: 0.6455 (mt-10) REVERT: C 37 ASP cc_start: 0.7192 (t70) cc_final: 0.6794 (m-30) REVERT: C 105 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8384 (mp) outliers start: 15 outliers final: 13 residues processed: 127 average time/residue: 0.1923 time to fit residues: 33.1991 Evaluate side-chains 125 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 251 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 95 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107813 restraints weight = 27047.764| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.36 r_work: 0.3234 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8316 Z= 0.092 Angle : 0.448 4.969 11267 Z= 0.238 Chirality : 0.038 0.146 1281 Planarity : 0.003 0.047 1435 Dihedral : 3.815 19.297 1156 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.26 % Allowed : 17.93 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.28), residues: 1028 helix: 2.43 (0.28), residues: 406 sheet: 0.03 (0.36), residues: 205 loop : -0.84 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 232 TYR 0.009 0.001 TYR C 185 PHE 0.009 0.001 PHE B 199 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 8314) covalent geometry : angle 0.44778 (11263) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.34772 ( 4) hydrogen bonds : bond 0.03756 ( 409) hydrogen bonds : angle 4.03042 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8377 (t0) cc_final: 0.7911 (p0) REVERT: B 215 GLU cc_start: 0.7587 (tt0) cc_final: 0.7299 (tt0) REVERT: G 14 LYS cc_start: 0.7212 (tptt) cc_final: 0.6655 (mtmt) REVERT: G 21 MET cc_start: 0.7409 (ttp) cc_final: 0.7090 (ttp) REVERT: G 22 GLU cc_start: 0.7331 (tt0) cc_final: 0.6514 (mt-10) REVERT: C 37 ASP cc_start: 0.7150 (t70) cc_final: 0.6871 (m-30) REVERT: C 105 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8403 (mp) outliers start: 11 outliers final: 9 residues processed: 125 average time/residue: 0.1916 time to fit residues: 32.1760 Evaluate side-chains 123 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105902 restraints weight = 27324.451| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.38 r_work: 0.3187 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8316 Z= 0.140 Angle : 0.479 5.683 11267 Z= 0.257 Chirality : 0.039 0.142 1281 Planarity : 0.003 0.049 1435 Dihedral : 3.971 21.005 1156 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.38 % Allowed : 18.39 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.27), residues: 1028 helix: 2.16 (0.27), residues: 413 sheet: 0.02 (0.37), residues: 199 loop : -1.00 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.014 0.001 TYR A 37 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8314) covalent geometry : angle 0.47940 (11263) SS BOND : bond 0.00245 ( 2) SS BOND : angle 0.42534 ( 4) hydrogen bonds : bond 0.04251 ( 409) hydrogen bonds : angle 4.13921 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8439 (t0) cc_final: 0.7833 (p0) REVERT: G 14 LYS cc_start: 0.7326 (tptt) cc_final: 0.6758 (mtmt) REVERT: G 22 GLU cc_start: 0.7391 (tt0) cc_final: 0.6559 (mt-10) REVERT: C 37 ASP cc_start: 0.7182 (t70) cc_final: 0.6897 (m-30) REVERT: C 105 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8421 (mp) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.1960 time to fit residues: 32.6500 Evaluate side-chains 125 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 99 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107355 restraints weight = 27134.524| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.39 r_work: 0.3227 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8316 Z= 0.100 Angle : 0.456 5.021 11267 Z= 0.243 Chirality : 0.038 0.145 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.845 19.510 1156 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.15 % Allowed : 18.51 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.27), residues: 1028 helix: 2.45 (0.27), residues: 406 sheet: 0.02 (0.36), residues: 200 loop : -0.90 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 62 TYR 0.010 0.001 TYR A 37 PHE 0.010 0.001 PHE B 199 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8314) covalent geometry : angle 0.45641 (11263) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.38183 ( 4) hydrogen bonds : bond 0.03820 ( 409) hydrogen bonds : angle 4.05867 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3537.01 seconds wall clock time: 60 minutes 21.23 seconds (3621.23 seconds total)