Starting phenix.real_space_refine on Wed Aug 5 06:56:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pa6_71434/08_2026/9pa6_71434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pa6_71434/08_2026/9pa6_71434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pa6_71434/08_2026/9pa6_71434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pa6_71434/08_2026/9pa6_71434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pa6_71434/08_2026/9pa6_71434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pa6_71434/08_2026/9pa6_71434.map" } resolution = 3.43 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= 0.021 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 60 5.16 5 C 5556 2.51 5 N 1457 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8705 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2186 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 274} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2, 'GLU:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1759 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2594 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1765 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.49, per 1000 atoms: 0.17 Number of scatterers: 8705 At special positions: 0 Unit cell: (127.512, 96.876, 117.576, 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 60 16.00 O 1632 8.00 N 1457 7.00 C 5556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 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: 0.57 Conformation dependent library (CDL) restraints added in 370.3 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 16 sheets defined 37.2% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 57 through 86 Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.724A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 4.365A pdb=" N MET A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 162 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.854A pdb=" N LEU A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.806A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 236 through 255 removed outlier: 3.960A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 300 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 305 through 332 removed outlier: 3.756A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.882A pdb=" N GLN B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.543A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 211' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.887A pdb=" N ASP B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 281 removed outlier: 4.091A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.825A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS B 286 " --> pdb=" O LEU B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 297 through 310 removed outlier: 3.719A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 352 Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.731A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 201 removed outlier: 3.677A pdb=" N GLY A 198 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 211 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.878A pdb=" N LEU B 268 " --> pdb=" O THR B 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.559A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.761A pdb=" N SER C 122 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 148 through 153 removed outlier: 3.724A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 190 through 192 removed outlier: 3.723A pdb=" N SER C 191 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.208A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.976A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR C 289 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.604A pdb=" N VAL E 12 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 17 through 21 removed outlier: 3.557A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.602A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.530A pdb=" N ARG E 148 " --> pdb=" O THR E 129 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE E 204 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AB7, first strand: chain 'E' and resid 177 through 178 409 hydrogen bonds defined for protein. 1173 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: 1.11 Time building geometry restraints manager: 0.75 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: 2772 1.34 - 1.46: 1839 1.46 - 1.58: 4185 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 8883 Sorted by residual: bond pdb=" CB GLU C 215 " pdb=" CG GLU C 215 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.18e+00 bond pdb=" CB ASN D 24 " pdb=" CG ASN D 24 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.20e+00 bond pdb=" CB ASP B 309 " pdb=" CG ASP B 309 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.88e+00 bond pdb=" CB ASP B 328 " pdb=" CG ASP B 328 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.85e+00 bond pdb=" C SER A 55 " pdb=" N PRO A 56 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.73e+00 ... (remaining 8878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11900 2.27 - 4.55: 119 4.55 - 6.82: 27 6.82 - 9.10: 9 9.10 - 11.37: 5 Bond angle restraints: 12060 Sorted by residual: angle pdb=" CB GLU C 215 " pdb=" CG GLU C 215 " pdb=" CD GLU C 215 " ideal model delta sigma weight residual 112.60 119.87 -7.27 1.70e+00 3.46e-01 1.83e+01 angle pdb=" CA GLU C 215 " pdb=" CB GLU C 215 " pdb=" CG GLU C 215 " ideal model delta sigma weight residual 114.10 122.01 -7.91 2.00e+00 2.50e-01 1.56e+01 angle pdb=" C ARG A 202 " pdb=" N GLU A 203 " pdb=" CA GLU A 203 " ideal model delta sigma weight residual 122.08 127.46 -5.38 1.47e+00 4.63e-01 1.34e+01 angle pdb=" C TYR B 296 " pdb=" N GLU B 297 " pdb=" CA GLU B 297 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 angle pdb=" CA LEU A 74 " pdb=" CB LEU A 74 " pdb=" CG LEU A 74 " ideal model delta sigma weight residual 116.30 127.67 -11.37 3.50e+00 8.16e-02 1.06e+01 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4440 17.58 - 35.17: 595 35.17 - 52.75: 173 52.75 - 70.33: 32 70.33 - 87.92: 14 Dihedral angle restraints: 5254 sinusoidal: 1969 harmonic: 3285 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO E 224 " pdb=" C PRO E 224 " pdb=" N LEU E 225 " pdb=" CA LEU E 225 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 210 " pdb=" CB CYS A 210 " ideal model delta sinusoidal sigma weight residual -86.00 -124.56 38.56 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 5251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 992 0.042 - 0.084: 316 0.084 - 0.125: 84 0.125 - 0.167: 8 0.167 - 0.209: 6 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CB THR E 91 " pdb=" CA THR E 91 " pdb=" OG1 THR E 91 " pdb=" CG2 THR E 91 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ASN A 77 " pdb=" N ASN A 77 " pdb=" C ASN A 77 " pdb=" CB ASN A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA MET E 83 " pdb=" N MET E 83 " pdb=" C MET E 83 " pdb=" CB MET E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 1403 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " 0.092 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PRO E 224 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 138 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO E 139 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO E 139 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO E 139 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 322 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" CG ASN A 322 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 322 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 322 " 0.014 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 394 2.72 - 3.27: 8395 3.27 - 3.81: 14584 3.81 - 4.36: 16854 4.36 - 4.90: 29733 Nonbonded interactions: 69960 Sorted by model distance: nonbonded pdb=" O ARG E 67 " pdb=" OG1 THR E 84 " model vdw 2.175 3.040 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.249 3.040 nonbonded pdb=" OG SER C 281 " pdb=" O HIS D 44 " model vdw 2.283 3.040 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.300 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.305 3.040 ... (remaining 69955 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.120 Find NCS groups from input model: 0.190 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8885 Z= 0.138 Angle : 0.665 11.374 12064 Z= 0.334 Chirality : 0.044 0.209 1406 Planarity : 0.006 0.141 1514 Dihedral : 17.794 87.918 3126 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.63 % Allowed : 34.46 % Favored : 64.90 % 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 are not related in a simple way. whole: -0.97 (0.25), residues: 1114 helix: 1.20 (0.25), residues: 388 sheet: -1.68 (0.34), residues: 255 loop : -1.57 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 18 TYR 0.015 0.001 TYR B 302 PHE 0.020 0.001 PHE E 200 TRP 0.009 0.001 TRP A 124 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 8883) covalent geometry : angle 0.66505 / 0.33 (12060) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 0.33770 / 0.19 ( 4) hydrogen bonds : bond 0.17462 / 11.93 ( 409) hydrogen bonds : angle 7.07221 / 5.03 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 293 PHE cc_start: 0.7829 (t80) cc_final: 0.7277 (t80) REVERT: A 324 SER cc_start: 0.8693 (t) cc_final: 0.8286 (p) REVERT: B 305 CYS cc_start: 0.8715 (t) cc_final: 0.8458 (m) outliers start: 6 outliers final: 5 residues processed: 148 average time/residue: 0.0734 time to fit residues: 16.2191 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 225 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN B 306 GLN B 331 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125655 restraints weight = 11160.843| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.65 r_work: 0.3296 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8885 Z= 0.132 Angle : 0.544 9.852 12064 Z= 0.282 Chirality : 0.040 0.154 1406 Planarity : 0.005 0.111 1514 Dihedral : 4.836 56.385 1220 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.02 % Allowed : 29.49 % Favored : 66.49 % 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 are not related in a simple way. whole: -0.43 (0.26), residues: 1114 helix: 1.95 (0.26), residues: 390 sheet: -1.54 (0.34), residues: 248 loop : -1.47 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.010 0.001 TYR E 178 PHE 0.012 0.001 PHE C 241 TRP 0.012 0.001 TRP C 211 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8883) covalent geometry : angle 0.54399 / 0.28 (12060) SS BOND : bond 0.00258 / 0.12 ( 2) SS BOND : angle 0.34294 / 0.19 ( 4) hydrogen bonds : bond 0.03834 / 2.55 ( 409) hydrogen bonds : angle 4.96489 / 3.56 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.222 Fit side-chains REVERT: A 95 ASN cc_start: 0.8116 (m110) cc_final: 0.7891 (m110) REVERT: A 183 TRP cc_start: 0.6674 (m-10) cc_final: 0.6251 (m100) REVERT: A 293 PHE cc_start: 0.7864 (t80) cc_final: 0.7337 (t80) REVERT: A 324 SER cc_start: 0.8673 (t) cc_final: 0.8297 (p) REVERT: B 23 LEU cc_start: 0.8376 (mt) cc_final: 0.8157 (mp) REVERT: B 350 ASP cc_start: 0.8134 (m-30) cc_final: 0.7801 (m-30) outliers start: 38 outliers final: 24 residues processed: 176 average time/residue: 0.0679 time to fit residues: 17.5979 Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123158 restraints weight = 11157.190| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.61 r_work: 0.3262 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8885 Z= 0.149 Angle : 0.548 9.839 12064 Z= 0.282 Chirality : 0.041 0.241 1406 Planarity : 0.004 0.088 1514 Dihedral : 4.514 52.706 1214 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.65 % Allowed : 29.18 % Favored : 66.17 % 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 are not related in a simple way. whole: -0.26 (0.26), residues: 1114 helix: 2.20 (0.26), residues: 387 sheet: -1.54 (0.34), residues: 241 loop : -1.40 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.014 0.001 TYR A 312 PHE 0.015 0.001 PHE C 241 TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8883) covalent geometry : angle 0.54798 / 0.28 (12060) SS BOND : bond 0.00245 / 0.12 ( 2) SS BOND : angle 0.26928 / 0.15 ( 4) hydrogen bonds : bond 0.03606 / 2.42 ( 409) hydrogen bonds : angle 4.73979 / 3.43 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.319 Fit side-chains REVERT: A 95 ASN cc_start: 0.8147 (m110) cc_final: 0.7906 (m110) REVERT: A 183 TRP cc_start: 0.6795 (m-10) cc_final: 0.6167 (m100) REVERT: A 324 SER cc_start: 0.8739 (t) cc_final: 0.8365 (p) REVERT: A 329 LEU cc_start: 0.7379 (tt) cc_final: 0.7021 (tt) REVERT: B 305 CYS cc_start: 0.8888 (t) cc_final: 0.8202 (t) REVERT: C 255 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7514 (mm) REVERT: E 171 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7700 (tt0) REVERT: E 218 MET cc_start: 0.7377 (ttt) cc_final: 0.7065 (ttt) outliers start: 44 outliers final: 29 residues processed: 188 average time/residue: 0.0738 time to fit residues: 20.2967 Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117105 restraints weight = 11440.438| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.78 r_work: 0.3159 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8885 Z= 0.272 Angle : 0.653 10.391 12064 Z= 0.337 Chirality : 0.044 0.187 1406 Planarity : 0.004 0.082 1514 Dihedral : 4.891 55.977 1214 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.77 % Allowed : 27.91 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.26), residues: 1114 helix: 2.07 (0.26), residues: 387 sheet: -1.84 (0.34), residues: 244 loop : -1.42 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.014 0.002 TYR B 302 PHE 0.023 0.002 PHE C 241 TRP 0.019 0.002 TRP E 47 HIS 0.007 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.27 ( 8883) covalent geometry : angle 0.65338 / 0.34 (12060) SS BOND : bond 0.00196 / 0.09 ( 2) SS BOND : angle 0.47095 / 0.26 ( 4) hydrogen bonds : bond 0.04056 / 2.67 ( 409) hydrogen bonds : angle 5.07603 / 3.66 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 0.331 Fit side-chains REVERT: A 95 ASN cc_start: 0.8239 (m110) cc_final: 0.7942 (m110) REVERT: A 121 MET cc_start: 0.6757 (mmm) cc_final: 0.6545 (mmm) REVERT: A 183 TRP cc_start: 0.7034 (m-10) cc_final: 0.6439 (m100) REVERT: A 329 LEU cc_start: 0.7488 (tt) cc_final: 0.7191 (tt) REVERT: B 305 CYS cc_start: 0.9009 (t) cc_final: 0.8401 (t) REVERT: B 354 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.5514 (m-80) REVERT: C 142 HIS cc_start: 0.9150 (OUTLIER) cc_final: 0.8885 (m-70) REVERT: C 215 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7335 (tm-30) REVERT: C 255 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7403 (mm) REVERT: E 76 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8388 (ttmm) REVERT: E 89 GLU cc_start: 0.8594 (pp20) cc_final: 0.8064 (pp20) REVERT: E 171 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7581 (tt0) outliers start: 64 outliers final: 38 residues processed: 198 average time/residue: 0.0771 time to fit residues: 22.3127 Evaluate side-chains 179 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125177 restraints weight = 10736.130| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.36 r_work: 0.3241 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8885 Z= 0.132 Angle : 0.561 10.016 12064 Z= 0.286 Chirality : 0.041 0.170 1406 Planarity : 0.004 0.061 1514 Dihedral : 4.569 55.271 1214 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.76 % Allowed : 29.70 % Favored : 65.54 % 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 are not related in a simple way. whole: -0.35 (0.26), residues: 1114 helix: 2.19 (0.26), residues: 389 sheet: -1.79 (0.34), residues: 239 loop : -1.44 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.011 0.001 TYR B 302 PHE 0.011 0.001 PHE A 337 TRP 0.009 0.001 TRP C 169 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8883) covalent geometry : angle 0.56126 / 0.29 (12060) SS BOND : bond 0.00156 / 0.07 ( 2) SS BOND : angle 0.35293 / 0.17 ( 4) hydrogen bonds : bond 0.03455 / 2.33 ( 409) hydrogen bonds : angle 4.77293 / 3.44 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.309 Fit side-chains REVERT: A 95 ASN cc_start: 0.8335 (m110) cc_final: 0.8023 (m110) REVERT: A 121 MET cc_start: 0.6789 (mmm) cc_final: 0.6567 (mmm) REVERT: A 170 ARG cc_start: 0.8498 (mtp-110) cc_final: 0.8137 (mtm180) REVERT: A 183 TRP cc_start: 0.7048 (OUTLIER) cc_final: 0.6463 (m100) REVERT: A 271 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6487 (tpt-90) REVERT: A 324 SER cc_start: 0.8733 (t) cc_final: 0.8410 (p) REVERT: A 329 LEU cc_start: 0.7538 (tt) cc_final: 0.7292 (tt) REVERT: B 305 CYS cc_start: 0.8975 (t) cc_final: 0.8361 (t) REVERT: C 215 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7492 (tm-30) REVERT: C 255 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7522 (mm) REVERT: E 76 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8373 (ttmm) REVERT: E 171 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7647 (tt0) outliers start: 45 outliers final: 31 residues processed: 178 average time/residue: 0.0787 time to fit residues: 20.2731 Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 59 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124300 restraints weight = 10756.592| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.43 r_work: 0.3240 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8885 Z= 0.149 Angle : 0.567 12.861 12064 Z= 0.288 Chirality : 0.041 0.154 1406 Planarity : 0.004 0.051 1514 Dihedral : 4.533 58.531 1214 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.60 % Allowed : 29.18 % Favored : 65.22 % 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 are not related in a simple way. whole: -0.36 (0.26), residues: 1114 helix: 2.21 (0.26), residues: 388 sheet: -1.81 (0.34), residues: 246 loop : -1.43 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 252 TYR 0.012 0.001 TYR B 302 PHE 0.013 0.001 PHE C 241 TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8883) covalent geometry : angle 0.56668 / 0.29 (12060) SS BOND : bond 0.00163 / 0.08 ( 2) SS BOND : angle 0.35934 / 0.18 ( 4) hydrogen bonds : bond 0.03429 / 2.31 ( 409) hydrogen bonds : angle 4.72861 / 3.41 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.325 Fit side-chains REVERT: A 95 ASN cc_start: 0.8368 (m110) cc_final: 0.8074 (m110) REVERT: A 121 MET cc_start: 0.6857 (mmm) cc_final: 0.6653 (mmm) REVERT: A 183 TRP cc_start: 0.7060 (OUTLIER) cc_final: 0.6456 (m100) REVERT: A 271 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6442 (tpt-90) REVERT: B 305 CYS cc_start: 0.8995 (t) cc_final: 0.8390 (t) REVERT: C 142 HIS cc_start: 0.9039 (OUTLIER) cc_final: 0.8648 (m-70) REVERT: C 215 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 255 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7597 (mm) REVERT: E 29 PHE cc_start: 0.8596 (t80) cc_final: 0.8275 (t80) REVERT: E 171 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7634 (tt0) outliers start: 53 outliers final: 36 residues processed: 185 average time/residue: 0.0688 time to fit residues: 18.5292 Evaluate side-chains 182 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 80 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124483 restraints weight = 10885.351| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.18 r_work: 0.3250 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8885 Z= 0.155 Angle : 0.581 11.563 12064 Z= 0.293 Chirality : 0.041 0.149 1406 Planarity : 0.004 0.047 1514 Dihedral : 4.480 55.974 1214 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.29 % Allowed : 29.49 % Favored : 65.22 % 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 are not related in a simple way. whole: -0.35 (0.26), residues: 1114 helix: 2.25 (0.26), residues: 387 sheet: -1.79 (0.34), residues: 247 loop : -1.45 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.012 0.001 TYR B 302 PHE 0.013 0.001 PHE C 241 TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 8883) covalent geometry : angle 0.58073 / 0.29 (12060) SS BOND : bond 0.00169 / 0.08 ( 2) SS BOND : angle 0.33960 / 0.17 ( 4) hydrogen bonds : bond 0.03409 / 2.31 ( 409) hydrogen bonds : angle 4.72914 / 3.41 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.254 Fit side-chains REVERT: A 95 ASN cc_start: 0.8350 (m110) cc_final: 0.8046 (m110) REVERT: A 176 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7952 (mmmt) REVERT: A 183 TRP cc_start: 0.7074 (OUTLIER) cc_final: 0.6423 (m100) REVERT: A 271 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6371 (tpt-90) REVERT: B 305 CYS cc_start: 0.8993 (t) cc_final: 0.8380 (t) REVERT: B 354 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: C 142 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8632 (m-70) REVERT: C 215 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7453 (tm-30) REVERT: C 255 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7504 (mm) REVERT: E 29 PHE cc_start: 0.8520 (t80) cc_final: 0.8276 (t80) REVERT: E 171 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7632 (tt0) outliers start: 50 outliers final: 39 residues processed: 186 average time/residue: 0.0692 time to fit residues: 18.6674 Evaluate side-chains 185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN B 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.170015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127166 restraints weight = 10692.165| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.18 r_work: 0.3269 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8885 Z= 0.123 Angle : 0.573 13.082 12064 Z= 0.286 Chirality : 0.041 0.144 1406 Planarity : 0.004 0.051 1514 Dihedral : 4.285 44.237 1214 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.76 % Allowed : 29.92 % Favored : 65.33 % 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 are not related in a simple way. whole: -0.31 (0.26), residues: 1114 helix: 2.27 (0.26), residues: 387 sheet: -1.68 (0.34), residues: 241 loop : -1.49 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.010 0.001 TYR B 302 PHE 0.011 0.001 PHE A 337 TRP 0.008 0.001 TRP C 211 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8883) covalent geometry : angle 0.57261 / 0.29 (12060) SS BOND : bond 0.00193 / 0.09 ( 2) SS BOND : angle 0.34139 / 0.17 ( 4) hydrogen bonds : bond 0.03292 / 2.25 ( 409) hydrogen bonds : angle 4.61103 / 3.32 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.345 Fit side-chains REVERT: A 95 ASN cc_start: 0.8389 (m110) cc_final: 0.8074 (m110) REVERT: A 170 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.8137 (mtm180) REVERT: A 176 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7978 (mmmt) REVERT: A 183 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: A 271 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6464 (tpt-90) REVERT: A 329 LEU cc_start: 0.7242 (tt) cc_final: 0.6901 (tt) REVERT: B 305 CYS cc_start: 0.8957 (t) cc_final: 0.8342 (t) REVERT: B 354 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: C 215 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 29 PHE cc_start: 0.8495 (t80) cc_final: 0.8237 (t80) REVERT: E 171 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7639 (tt0) outliers start: 45 outliers final: 33 residues processed: 179 average time/residue: 0.0678 time to fit residues: 17.8531 Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 0.0030 chunk 23 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 73 optimal weight: 0.9980 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.171924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129644 restraints weight = 10628.923| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.15 r_work: 0.3316 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8885 Z= 0.106 Angle : 0.573 13.645 12064 Z= 0.283 Chirality : 0.040 0.208 1406 Planarity : 0.004 0.054 1514 Dihedral : 3.867 27.813 1211 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.33 % Allowed : 30.44 % Favored : 65.22 % 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 are not related in a simple way. whole: -0.21 (0.26), residues: 1114 helix: 2.29 (0.26), residues: 389 sheet: -1.54 (0.35), residues: 237 loop : -1.45 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.009 0.001 TYR E 178 PHE 0.011 0.001 PHE A 337 TRP 0.009 0.001 TRP C 82 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8883) covalent geometry : angle 0.57341 / 0.28 (12060) SS BOND : bond 0.00237 / 0.11 ( 2) SS BOND : angle 0.33844 / 0.17 ( 4) hydrogen bonds : bond 0.03101 / 2.16 ( 409) hydrogen bonds : angle 4.46807 / 3.22 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.312 Fit side-chains REVERT: A 95 ASN cc_start: 0.8354 (m110) cc_final: 0.8051 (m110) REVERT: A 176 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7975 (mmmt) REVERT: A 183 TRP cc_start: 0.7045 (OUTLIER) cc_final: 0.6602 (m-10) REVERT: A 271 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6444 (tpt-90) REVERT: A 293 PHE cc_start: 0.7847 (t80) cc_final: 0.7288 (t80) REVERT: A 329 LEU cc_start: 0.7073 (tt) cc_final: 0.6731 (tt) REVERT: B 305 CYS cc_start: 0.8923 (t) cc_final: 0.8293 (t) REVERT: B 354 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5337 (m-80) REVERT: C 215 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7501 (tm-30) REVERT: C 255 LEU cc_start: 0.7863 (mm) cc_final: 0.7572 (mm) REVERT: E 29 PHE cc_start: 0.8321 (t80) cc_final: 0.8002 (t80) REVERT: E 89 GLU cc_start: 0.8602 (pp20) cc_final: 0.8038 (pp20) outliers start: 41 outliers final: 31 residues processed: 181 average time/residue: 0.0638 time to fit residues: 16.8610 Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129286 restraints weight = 10690.300| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.07 r_work: 0.3305 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8885 Z= 0.121 Angle : 0.609 13.702 12064 Z= 0.298 Chirality : 0.041 0.232 1406 Planarity : 0.004 0.056 1514 Dihedral : 3.863 26.328 1211 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.12 % Allowed : 30.66 % Favored : 65.22 % 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 are not related in a simple way. whole: -0.26 (0.26), residues: 1114 helix: 2.30 (0.26), residues: 390 sheet: -1.65 (0.34), residues: 252 loop : -1.44 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.010 0.001 TYR B 302 PHE 0.011 0.001 PHE A 337 TRP 0.007 0.001 TRP C 82 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8883) covalent geometry : angle 0.60931 / 0.30 (12060) SS BOND : bond 0.00223 / 0.11 ( 2) SS BOND : angle 0.33539 / 0.17 ( 4) hydrogen bonds : bond 0.03168 / 2.19 ( 409) hydrogen bonds : angle 4.48558 / 3.23 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.345 Fit side-chains REVERT: A 95 ASN cc_start: 0.8340 (m110) cc_final: 0.8020 (m110) REVERT: A 183 TRP cc_start: 0.7030 (OUTLIER) cc_final: 0.6669 (m-10) REVERT: A 226 MET cc_start: 0.8043 (ppp) cc_final: 0.7825 (ppp) REVERT: A 271 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6395 (tpt-90) REVERT: A 293 PHE cc_start: 0.7850 (t80) cc_final: 0.7320 (t80) REVERT: A 329 LEU cc_start: 0.7034 (tt) cc_final: 0.6695 (tt) REVERT: B 305 CYS cc_start: 0.8942 (t) cc_final: 0.8322 (t) REVERT: B 354 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5384 (m-80) REVERT: C 215 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7508 (tm-30) REVERT: E 29 PHE cc_start: 0.8286 (t80) cc_final: 0.7986 (t80) REVERT: E 89 GLU cc_start: 0.8606 (pp20) cc_final: 0.8035 (pp20) outliers start: 39 outliers final: 34 residues processed: 180 average time/residue: 0.0767 time to fit residues: 20.0643 Evaluate side-chains 182 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN B 195 HIS B 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.170669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129027 restraints weight = 10577.040| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.05 r_work: 0.3287 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8885 Z= 0.127 Angle : 0.606 13.669 12064 Z= 0.295 Chirality : 0.041 0.221 1406 Planarity : 0.004 0.057 1514 Dihedral : 3.874 26.503 1211 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.02 % Allowed : 30.76 % Favored : 65.22 % 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 are not related in a simple way. whole: -0.26 (0.26), residues: 1114 helix: 2.30 (0.26), residues: 390 sheet: -1.67 (0.34), residues: 247 loop : -1.45 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.010 0.001 TYR B 302 PHE 0.011 0.001 PHE B 199 TRP 0.008 0.001 TRP C 211 HIS 0.004 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8883) covalent geometry : angle 0.60573 / 0.30 (12060) SS BOND : bond 0.00216 / 0.10 ( 2) SS BOND : angle 0.32311 / 0.16 ( 4) hydrogen bonds : bond 0.03186 / 2.20 ( 409) hydrogen bonds : angle 4.48757 / 3.23 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.49 seconds wall clock time: 35 minutes 59.35 seconds (2159.35 seconds total)