Starting phenix.real_space_refine on Sat Aug 23 02:30:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g94_29861/08_2025/8g94_29861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g94_29861/08_2025/8g94_29861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g94_29861/08_2025/8g94_29861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g94_29861/08_2025/8g94_29861.map" model { file = "/net/cci-nas-00/data/ceres_data/8g94_29861/08_2025/8g94_29861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g94_29861/08_2025/8g94_29861.cif" } resolution = 3.15 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5891 2.51 5 N 1565 2.21 5 O 1701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 9222 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2316 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 2 Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1780 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "F" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 179 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 134 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 1.72, per 1000 atoms: 0.19 Number of scatterers: 9222 At special positions: 0 Unit cell: (89.64, 118.69, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1701 8.00 N 1565 7.00 C 5891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 0.60 Conformation dependent library (CDL) restraints added in 242.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 38.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.280A pdb=" N ILE A 25 " --> pdb=" O ASN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.749A pdb=" N ILE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.881A pdb=" N TYR A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.561A pdb=" N LEU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 235 removed outlier: 3.784A pdb=" N LEU A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 281 removed outlier: 3.577A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.855A pdb=" N PHE A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.608A pdb=" N ALA A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.728A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.599A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.675A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.572A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 295 through 310 Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.405A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.606A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 24 removed outlier: 3.622A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.285A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'F' and resid 41 through 64 Processing helix chain 'G' and resid 41 through 64 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.564A pdb=" N LEU B 194 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.774A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.771A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.588A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.820A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.494A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.636A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.375A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.536A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1338 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: 1.30 Time building geometry restraints manager: 0.81 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: 2929 1.34 - 1.46: 1647 1.46 - 1.57: 4729 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9398 Sorted by residual: bond pdb=" CG LEU C 70 " pdb=" CD2 LEU C 70 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CB ASP C 163 " pdb=" CG ASP C 163 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.02e+00 bond pdb=" CG1 ILE C 81 " pdb=" CD1 ILE C 81 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C PHE A 76 " pdb=" O PHE A 76 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.24e-02 6.50e+03 1.66e+00 bond pdb=" CG PHE C 234 " pdb=" CD1 PHE C 234 " ideal model delta sigma weight residual 1.384 1.358 0.026 2.10e-02 2.27e+03 1.56e+00 ... (remaining 9393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12336 1.75 - 3.49: 328 3.49 - 5.24: 37 5.24 - 6.98: 13 6.98 - 8.73: 8 Bond angle restraints: 12722 Sorted by residual: angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C LYS A 75 " pdb=" N PHE A 76 " pdb=" CA PHE A 76 " ideal model delta sigma weight residual 120.38 126.88 -6.50 1.46e+00 4.69e-01 1.98e+01 angle pdb=" N PHE A 76 " pdb=" CA PHE A 76 " pdb=" C PHE A 76 " ideal model delta sigma weight residual 111.75 117.17 -5.42 1.28e+00 6.10e-01 1.80e+01 angle pdb=" N SER C 334 " pdb=" CA SER C 334 " pdb=" C SER C 334 " ideal model delta sigma weight residual 112.24 117.43 -5.19 1.28e+00 6.10e-01 1.64e+01 angle pdb=" C TYR A 81 " pdb=" N TYR A 82 " pdb=" CA TYR A 82 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 ... (remaining 12717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5120 17.91 - 35.81: 391 35.81 - 53.72: 60 53.72 - 71.62: 12 71.62 - 89.53: 3 Dihedral angle restraints: 5586 sinusoidal: 2140 harmonic: 3446 Sorted by residual: dihedral pdb=" CA ARG C 304 " pdb=" C ARG C 304 " pdb=" N ALA C 305 " pdb=" CA ALA C 305 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1251 0.063 - 0.127: 212 0.127 - 0.190: 15 0.190 - 0.254: 2 0.254 - 0.317: 1 Chirality restraints: 1481 Sorted by residual: chirality pdb=" CA SER C 334 " pdb=" N SER C 334 " pdb=" C SER C 334 " pdb=" CB SER C 334 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU B 353 " pdb=" CB LEU B 353 " pdb=" CD1 LEU B 353 " pdb=" CD2 LEU B 353 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PHE A 76 " pdb=" N PHE A 76 " pdb=" C PHE A 76 " pdb=" CB PHE A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1478 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 234 " 0.022 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE C 234 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 234 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 234 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 234 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 64 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C VAL E 64 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL E 64 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS E 65 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 113 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.55e+00 pdb=" N PRO A 114 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.030 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1159 2.74 - 3.28: 8986 3.28 - 3.82: 15340 3.82 - 4.36: 18501 4.36 - 4.90: 32119 Nonbonded interactions: 76105 Sorted by model distance: nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.206 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.207 3.040 nonbonded pdb=" O LEU A 174 " pdb=" OH TYR A 202 " model vdw 2.247 3.040 nonbonded pdb=" O ARG C 68 " pdb=" OG SER C 84 " model vdw 2.281 3.040 nonbonded pdb=" O VAL F 48 " pdb=" OG1 THR F 52 " model vdw 2.282 3.040 ... (remaining 76100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.400 Find NCS groups from input model: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.006 0.061 9399 Z= 0.264 Angle : 0.718 8.730 12724 Z= 0.396 Chirality : 0.047 0.317 1481 Planarity : 0.005 0.053 1586 Dihedral : 13.016 89.531 3355 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.32 (0.22), residues: 1163 helix: -0.70 (0.22), residues: 423 sheet: -1.92 (0.28), residues: 286 loop : -1.90 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 190 TYR 0.014 0.002 TYR E 178 PHE 0.044 0.002 PHE C 234 TRP 0.032 0.002 TRP C 339 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 9398) covalent geometry : angle 0.71850 (12722) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.69842 ( 2) hydrogen bonds : bond 0.15093 ( 469) hydrogen bonds : angle 6.08223 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8482 (mttm) cc_final: 0.7811 (ptmm) REVERT: A 182 TRP cc_start: 0.7474 (t-100) cc_final: 0.6963 (t60) REVERT: B 9 ASP cc_start: 0.8477 (m-30) cc_final: 0.8163 (m-30) REVERT: C 9 GLN cc_start: 0.8310 (pp30) cc_final: 0.7995 (pp30) REVERT: C 10 GLU cc_start: 0.8620 (tt0) cc_final: 0.8053 (tt0) REVERT: C 67 SER cc_start: 0.9180 (m) cc_final: 0.8948 (t) REVERT: C 214 ARG cc_start: 0.8202 (mpp80) cc_final: 0.7971 (mtt180) REVERT: C 262 MET cc_start: 0.8177 (ttm) cc_final: 0.7762 (ttm) REVERT: D 11 GLN cc_start: 0.8874 (mm110) cc_final: 0.8663 (tp40) REVERT: D 14 LYS cc_start: 0.9178 (tppp) cc_final: 0.8821 (ttpt) REVERT: D 20 LYS cc_start: 0.9104 (mttm) cc_final: 0.8700 (mttm) REVERT: E 87 ARG cc_start: 0.8272 (mpp80) cc_final: 0.7778 (mtt90) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1068 time to fit residues: 23.0329 Evaluate side-chains 132 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN A 303 ASN A 315 ASN B 213 HIS B 255 ASN B 306 GLN B 331 ASN B 333 GLN C 16 ASN C 91 HIS C 156 GLN C 259 GLN D 59 ASN E 39 GLN F 47 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.070562 restraints weight = 16316.192| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.65 r_work: 0.2754 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9399 Z= 0.129 Angle : 0.554 8.353 12724 Z= 0.290 Chirality : 0.041 0.155 1481 Planarity : 0.004 0.051 1586 Dihedral : 4.393 20.201 1278 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 8.70 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.24), residues: 1163 helix: 0.87 (0.25), residues: 426 sheet: -1.36 (0.30), residues: 259 loop : -1.53 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.015 0.001 TYR E 215 PHE 0.021 0.001 PHE A 58 TRP 0.032 0.001 TRP C 339 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9398) covalent geometry : angle 0.55353 (12722) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.85559 ( 2) hydrogen bonds : bond 0.03999 ( 469) hydrogen bonds : angle 4.65081 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8353 (mttm) cc_final: 0.7581 (tttp) REVERT: A 182 TRP cc_start: 0.7498 (t-100) cc_final: 0.6598 (t60) REVERT: A 277 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7458 (mm) REVERT: A 295 TYR cc_start: 0.6918 (m-80) cc_final: 0.6331 (m-80) REVERT: B 353 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8735 (mm) REVERT: C 9 GLN cc_start: 0.8259 (pp30) cc_final: 0.8007 (pp30) REVERT: C 37 ILE cc_start: 0.9494 (mt) cc_final: 0.9139 (tt) REVERT: C 214 ARG cc_start: 0.8819 (mpp80) cc_final: 0.8500 (mmt-90) REVERT: C 217 MET cc_start: 0.9037 (ptp) cc_final: 0.8606 (ppp) REVERT: C 262 MET cc_start: 0.9002 (ttm) cc_final: 0.8632 (ttm) REVERT: D 14 LYS cc_start: 0.9161 (tppp) cc_final: 0.8894 (ttpt) REVERT: D 18 GLN cc_start: 0.8760 (tp40) cc_final: 0.8228 (tp-100) REVERT: D 20 LYS cc_start: 0.9078 (mttm) cc_final: 0.8797 (mttm) REVERT: D 22 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8062 (mt-10) REVERT: E 171 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8681 (mt0) outliers start: 26 outliers final: 10 residues processed: 154 average time/residue: 0.0827 time to fit residues: 17.5334 Evaluate side-chains 142 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN D 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.069939 restraints weight = 16473.935| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.67 r_work: 0.2736 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9399 Z= 0.151 Angle : 0.529 7.089 12724 Z= 0.278 Chirality : 0.041 0.166 1481 Planarity : 0.004 0.049 1586 Dihedral : 4.233 19.819 1278 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.40 % Allowed : 11.20 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.40 (0.24), residues: 1163 helix: 1.42 (0.25), residues: 423 sheet: -1.10 (0.31), residues: 261 loop : -1.27 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.012 0.001 TYR E 178 PHE 0.023 0.001 PHE A 58 TRP 0.025 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9398) covalent geometry : angle 0.52923 (12722) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.57006 ( 2) hydrogen bonds : bond 0.03743 ( 469) hydrogen bonds : angle 4.39884 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8313 (mt0) cc_final: 0.8053 (mt0) REVERT: A 148 LYS cc_start: 0.8348 (mttm) cc_final: 0.7541 (tttp) REVERT: A 182 TRP cc_start: 0.7491 (t-100) cc_final: 0.7186 (t60) REVERT: B 353 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8757 (mm) REVERT: C 9 GLN cc_start: 0.8309 (pp30) cc_final: 0.8064 (pp30) REVERT: C 37 ILE cc_start: 0.9471 (mt) cc_final: 0.9158 (tt) REVERT: C 214 ARG cc_start: 0.8837 (mpp80) cc_final: 0.8561 (mmt-90) REVERT: C 217 MET cc_start: 0.9060 (ptp) cc_final: 0.8641 (ppp) REVERT: C 246 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8536 (m-30) REVERT: C 262 MET cc_start: 0.8995 (ttm) cc_final: 0.8599 (ttm) REVERT: D 14 LYS cc_start: 0.9165 (tppp) cc_final: 0.8927 (ttpt) REVERT: D 18 GLN cc_start: 0.8805 (tp40) cc_final: 0.8462 (tp40) REVERT: D 20 LYS cc_start: 0.9103 (mttm) cc_final: 0.8827 (mttm) REVERT: D 58 GLU cc_start: 0.8591 (pm20) cc_final: 0.8263 (pm20) outliers start: 24 outliers final: 14 residues processed: 148 average time/residue: 0.0817 time to fit residues: 16.9341 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 0.0670 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070895 restraints weight = 16495.819| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.66 r_work: 0.2765 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9399 Z= 0.111 Angle : 0.503 7.354 12724 Z= 0.264 Chirality : 0.040 0.176 1481 Planarity : 0.003 0.047 1586 Dihedral : 4.036 16.982 1278 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.30 % Allowed : 12.30 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.09 (0.25), residues: 1163 helix: 1.71 (0.25), residues: 423 sheet: -0.97 (0.32), residues: 263 loop : -1.11 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.012 0.001 TYR C 59 PHE 0.022 0.001 PHE A 58 TRP 0.024 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9398) covalent geometry : angle 0.50343 (12722) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.16229 ( 2) hydrogen bonds : bond 0.03450 ( 469) hydrogen bonds : angle 4.24108 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8284 (mt0) cc_final: 0.7996 (mt0) REVERT: A 148 LYS cc_start: 0.8330 (mttm) cc_final: 0.7556 (tttp) REVERT: A 180 MET cc_start: 0.8066 (mtm) cc_final: 0.7693 (ppp) REVERT: A 182 TRP cc_start: 0.7300 (t-100) cc_final: 0.6851 (t60) REVERT: A 277 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7563 (mm) REVERT: B 306 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8188 (mm-40) REVERT: C 9 GLN cc_start: 0.8300 (pp30) cc_final: 0.8057 (pp30) REVERT: C 37 ILE cc_start: 0.9458 (mt) cc_final: 0.9074 (tt) REVERT: C 214 ARG cc_start: 0.8819 (mpp80) cc_final: 0.8540 (mmt-90) REVERT: C 217 MET cc_start: 0.9044 (ptp) cc_final: 0.8658 (ppp) REVERT: C 246 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8407 (m-30) REVERT: C 262 MET cc_start: 0.8992 (ttm) cc_final: 0.8581 (ttm) REVERT: D 18 GLN cc_start: 0.8737 (tp40) cc_final: 0.8342 (tp40) REVERT: D 20 LYS cc_start: 0.9112 (mttm) cc_final: 0.8835 (mttm) REVERT: D 22 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7829 (mt-10) REVERT: D 58 GLU cc_start: 0.8583 (pm20) cc_final: 0.8252 (pm20) REVERT: E 171 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8568 (mm-40) outliers start: 23 outliers final: 11 residues processed: 155 average time/residue: 0.0933 time to fit residues: 19.8031 Evaluate side-chains 147 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 0.0770 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067596 restraints weight = 16486.725| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.65 r_work: 0.2690 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9399 Z= 0.235 Angle : 0.569 6.858 12724 Z= 0.299 Chirality : 0.042 0.202 1481 Planarity : 0.004 0.046 1586 Dihedral : 4.257 21.471 1278 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.00 % Allowed : 12.90 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.05 (0.25), residues: 1163 helix: 1.82 (0.25), residues: 423 sheet: -0.86 (0.32), residues: 271 loop : -1.05 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.014 0.002 TYR E 163 PHE 0.020 0.001 PHE A 58 TRP 0.017 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 9398) covalent geometry : angle 0.56890 (12722) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.41325 ( 2) hydrogen bonds : bond 0.03731 ( 469) hydrogen bonds : angle 4.35395 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8307 (mt0) cc_final: 0.8012 (mt0) REVERT: A 148 LYS cc_start: 0.8321 (mttm) cc_final: 0.7505 (tttp) REVERT: A 180 MET cc_start: 0.8169 (mtm) cc_final: 0.7388 (ppp) REVERT: A 182 TRP cc_start: 0.7348 (t-100) cc_final: 0.6936 (t60) REVERT: A 277 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7523 (mm) REVERT: B 306 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8192 (mm-40) REVERT: C 9 GLN cc_start: 0.8294 (pp30) cc_final: 0.8005 (pp30) REVERT: C 37 ILE cc_start: 0.9503 (mt) cc_final: 0.9174 (tt) REVERT: C 214 ARG cc_start: 0.8833 (mpp80) cc_final: 0.8549 (mmt-90) REVERT: C 217 MET cc_start: 0.9045 (ptp) cc_final: 0.8648 (ppp) REVERT: C 262 MET cc_start: 0.8999 (ttm) cc_final: 0.8629 (ttm) REVERT: D 18 GLN cc_start: 0.8743 (tp40) cc_final: 0.8344 (tp40) REVERT: D 20 LYS cc_start: 0.9076 (mttm) cc_final: 0.8808 (mttm) REVERT: D 22 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7841 (mt-10) REVERT: D 58 GLU cc_start: 0.8615 (pm20) cc_final: 0.8232 (pm20) outliers start: 30 outliers final: 18 residues processed: 148 average time/residue: 0.0844 time to fit residues: 17.0885 Evaluate side-chains 151 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 59 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.070635 restraints weight = 16425.520| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.64 r_work: 0.2752 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9399 Z= 0.109 Angle : 0.509 7.464 12724 Z= 0.266 Chirality : 0.040 0.187 1481 Planarity : 0.003 0.046 1586 Dihedral : 3.995 17.222 1278 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.00 % Allowed : 13.60 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.25 (0.25), residues: 1163 helix: 2.00 (0.25), residues: 423 sheet: -0.81 (0.32), residues: 268 loop : -0.89 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 8 TYR 0.010 0.001 TYR E 178 PHE 0.025 0.001 PHE A 58 TRP 0.020 0.001 TRP C 339 HIS 0.003 0.000 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9398) covalent geometry : angle 0.50904 (12722) SS BOND : bond 0.00279 ( 1) SS BOND : angle 0.28434 ( 2) hydrogen bonds : bond 0.03369 ( 469) hydrogen bonds : angle 4.19098 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8299 (mt0) cc_final: 0.7970 (mt0) REVERT: A 148 LYS cc_start: 0.8302 (mttm) cc_final: 0.7503 (tttp) REVERT: A 180 MET cc_start: 0.8142 (mtm) cc_final: 0.6916 (ppp) REVERT: A 182 TRP cc_start: 0.7288 (t-100) cc_final: 0.6944 (t60) REVERT: A 277 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7515 (mm) REVERT: B 306 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8201 (mm-40) REVERT: C 9 GLN cc_start: 0.8296 (pp30) cc_final: 0.8030 (pp30) REVERT: C 37 ILE cc_start: 0.9455 (mt) cc_final: 0.9071 (tt) REVERT: C 214 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8524 (mmt-90) REVERT: C 217 MET cc_start: 0.9046 (ptp) cc_final: 0.8698 (ppp) REVERT: C 262 MET cc_start: 0.8939 (ttm) cc_final: 0.8576 (ttm) REVERT: D 18 GLN cc_start: 0.8757 (tp40) cc_final: 0.8334 (tp40) REVERT: D 20 LYS cc_start: 0.9083 (mttm) cc_final: 0.8814 (mttm) REVERT: D 22 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7846 (mt-10) REVERT: D 58 GLU cc_start: 0.8581 (pm20) cc_final: 0.8249 (pm20) outliers start: 20 outliers final: 13 residues processed: 154 average time/residue: 0.0926 time to fit residues: 19.5108 Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 99 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 100 optimal weight: 0.0020 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.070438 restraints weight = 16442.608| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.65 r_work: 0.2754 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9399 Z= 0.122 Angle : 0.525 9.738 12724 Z= 0.272 Chirality : 0.040 0.190 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.930 16.786 1278 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.30 % Allowed : 13.80 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.34 (0.25), residues: 1163 helix: 2.03 (0.25), residues: 432 sheet: -0.77 (0.32), residues: 268 loop : -0.85 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.019 0.001 TYR B 230 PHE 0.022 0.001 PHE A 58 TRP 0.020 0.001 TRP C 339 HIS 0.002 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9398) covalent geometry : angle 0.52483 (12722) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.12047 ( 2) hydrogen bonds : bond 0.03334 ( 469) hydrogen bonds : angle 4.16460 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8227 (mt0) cc_final: 0.7902 (mt0) REVERT: A 180 MET cc_start: 0.8153 (mtm) cc_final: 0.7159 (ppp) REVERT: A 182 TRP cc_start: 0.7252 (t-100) cc_final: 0.6973 (t60) REVERT: A 277 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7530 (mm) REVERT: B 298 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8179 (pp20) REVERT: B 306 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8161 (mm-40) REVERT: C 37 ILE cc_start: 0.9457 (mt) cc_final: 0.9115 (tt) REVERT: C 214 ARG cc_start: 0.8813 (mpp80) cc_final: 0.8565 (mmt-90) REVERT: C 217 MET cc_start: 0.9032 (ptp) cc_final: 0.8680 (ppp) REVERT: C 262 MET cc_start: 0.8937 (ttm) cc_final: 0.8589 (ttm) REVERT: D 18 GLN cc_start: 0.8754 (tp40) cc_final: 0.8316 (tp40) REVERT: D 20 LYS cc_start: 0.9081 (mttm) cc_final: 0.8799 (mttm) REVERT: D 22 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 58 GLU cc_start: 0.8595 (pm20) cc_final: 0.8229 (pm20) REVERT: E 171 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8555 (mm-40) outliers start: 23 outliers final: 14 residues processed: 145 average time/residue: 0.0937 time to fit residues: 18.8246 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 69 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.071540 restraints weight = 16296.056| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.66 r_work: 0.2773 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9399 Z= 0.109 Angle : 0.511 7.847 12724 Z= 0.267 Chirality : 0.040 0.189 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.843 16.657 1278 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.20 % Allowed : 14.00 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.44 (0.25), residues: 1163 helix: 2.08 (0.25), residues: 432 sheet: -0.72 (0.32), residues: 268 loop : -0.75 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.010 0.001 TYR E 178 PHE 0.020 0.001 PHE A 58 TRP 0.020 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9398) covalent geometry : angle 0.51083 (12722) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.15651 ( 2) hydrogen bonds : bond 0.03230 ( 469) hydrogen bonds : angle 4.09419 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8161 (mt0) cc_final: 0.7843 (mt0) REVERT: A 180 MET cc_start: 0.8123 (mtm) cc_final: 0.7127 (ppp) REVERT: A 182 TRP cc_start: 0.7248 (t-100) cc_final: 0.6979 (t60) REVERT: A 277 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7491 (mm) REVERT: B 298 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8216 (pp20) REVERT: B 306 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8141 (mm-40) REVERT: C 37 ILE cc_start: 0.9454 (mt) cc_final: 0.9139 (tt) REVERT: C 130 GLU cc_start: 0.9201 (mp0) cc_final: 0.8927 (mp0) REVERT: C 217 MET cc_start: 0.9034 (ptp) cc_final: 0.8714 (ppp) REVERT: C 262 MET cc_start: 0.8919 (ttm) cc_final: 0.8572 (ttm) REVERT: D 13 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8350 (ttm110) REVERT: D 18 GLN cc_start: 0.8730 (tp40) cc_final: 0.8292 (tp40) REVERT: D 20 LYS cc_start: 0.9066 (mttm) cc_final: 0.8775 (mttm) REVERT: D 22 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7838 (mt-10) REVERT: D 58 GLU cc_start: 0.8600 (pm20) cc_final: 0.8233 (pm20) REVERT: E 171 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8574 (mm-40) outliers start: 22 outliers final: 13 residues processed: 149 average time/residue: 0.0858 time to fit residues: 17.6354 Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 0.0030 chunk 107 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.072209 restraints weight = 16262.499| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.69 r_work: 0.2785 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9399 Z= 0.114 Angle : 0.525 8.000 12724 Z= 0.272 Chirality : 0.040 0.197 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.805 16.370 1278 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.90 % Allowed : 14.50 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.54 (0.25), residues: 1163 helix: 2.13 (0.25), residues: 433 sheet: -0.67 (0.32), residues: 268 loop : -0.66 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.011 0.001 TYR C 59 PHE 0.019 0.001 PHE A 58 TRP 0.020 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9398) covalent geometry : angle 0.52484 (12722) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.13091 ( 2) hydrogen bonds : bond 0.03211 ( 469) hydrogen bonds : angle 4.07170 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8157 (mt0) cc_final: 0.7862 (mt0) REVERT: A 180 MET cc_start: 0.8174 (mtm) cc_final: 0.7097 (ppp) REVERT: A 182 TRP cc_start: 0.7248 (t-100) cc_final: 0.7009 (t60) REVERT: A 277 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7467 (mm) REVERT: B 298 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8216 (pp20) REVERT: C 37 ILE cc_start: 0.9437 (mt) cc_final: 0.9169 (tt) REVERT: C 130 GLU cc_start: 0.9194 (mp0) cc_final: 0.8964 (mp0) REVERT: C 217 MET cc_start: 0.9011 (ptp) cc_final: 0.8717 (ppp) REVERT: C 262 MET cc_start: 0.8921 (ttm) cc_final: 0.8595 (ttm) REVERT: D 13 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8369 (ttm110) REVERT: D 18 GLN cc_start: 0.8738 (tp40) cc_final: 0.8325 (tp40) REVERT: D 20 LYS cc_start: 0.9098 (mttm) cc_final: 0.8806 (mttm) REVERT: D 22 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7804 (mt-10) REVERT: D 58 GLU cc_start: 0.8586 (pm20) cc_final: 0.8230 (pm20) REVERT: E 171 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8531 (mm-40) outliers start: 19 outliers final: 14 residues processed: 147 average time/residue: 0.0860 time to fit residues: 17.6922 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.069524 restraints weight = 16421.321| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.65 r_work: 0.2730 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9399 Z= 0.167 Angle : 0.574 16.105 12724 Z= 0.292 Chirality : 0.042 0.256 1481 Planarity : 0.003 0.044 1586 Dihedral : 3.965 17.853 1278 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.70 % Allowed : 14.80 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.52 (0.25), residues: 1163 helix: 2.11 (0.25), residues: 433 sheet: -0.75 (0.31), residues: 272 loop : -0.61 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.012 0.001 TYR E 178 PHE 0.018 0.001 PHE A 65 TRP 0.017 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9398) covalent geometry : angle 0.57361 (12722) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.34382 ( 2) hydrogen bonds : bond 0.03439 ( 469) hydrogen bonds : angle 4.18370 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8201 (mt0) cc_final: 0.7851 (mt0) REVERT: A 180 MET cc_start: 0.8139 (mtm) cc_final: 0.7144 (ppp) REVERT: A 182 TRP cc_start: 0.7240 (t-100) cc_final: 0.7006 (t60) REVERT: A 277 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7452 (mm) REVERT: B 298 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: C 37 ILE cc_start: 0.9464 (mt) cc_final: 0.9101 (tt) REVERT: C 130 GLU cc_start: 0.9208 (mp0) cc_final: 0.8967 (mp0) REVERT: C 217 MET cc_start: 0.9028 (ptp) cc_final: 0.8694 (ppp) REVERT: C 262 MET cc_start: 0.8936 (ttm) cc_final: 0.8615 (ttm) REVERT: D 13 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8346 (ttm110) REVERT: D 18 GLN cc_start: 0.8723 (tp40) cc_final: 0.8244 (tp40) REVERT: D 22 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 58 GLU cc_start: 0.8624 (pm20) cc_final: 0.8245 (pm20) outliers start: 17 outliers final: 13 residues processed: 139 average time/residue: 0.1031 time to fit residues: 19.7684 Evaluate side-chains 141 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.070065 restraints weight = 16139.483| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.65 r_work: 0.2737 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9399 Z= 0.159 Angle : 0.574 15.851 12724 Z= 0.292 Chirality : 0.042 0.267 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.986 17.465 1278 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.70 % Allowed : 15.70 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.54 (0.25), residues: 1163 helix: 2.12 (0.25), residues: 433 sheet: -0.74 (0.31), residues: 271 loop : -0.58 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.017 0.001 TYR B 287 PHE 0.019 0.001 PHE A 65 TRP 0.018 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9398) covalent geometry : angle 0.57422 (12722) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.26134 ( 2) hydrogen bonds : bond 0.03423 ( 469) hydrogen bonds : angle 4.18591 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.75 seconds wall clock time: 46 minutes 34.57 seconds (2794.57 seconds total)