Starting phenix.real_space_refine on Fri Mar 14 07:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5f_38933/03_2025/8y5f_38933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5f_38933/03_2025/8y5f_38933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5f_38933/03_2025/8y5f_38933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5f_38933/03_2025/8y5f_38933.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5f_38933/03_2025/8y5f_38933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5f_38933/03_2025/8y5f_38933.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.042 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 6381 2.51 5 N 1646 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9846 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2876 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1936 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2862 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 13, 'TRANS': 344} Time building chain proxies: 6.19, per 1000 atoms: 0.63 Number of scatterers: 9846 At special positions: 0 Unit cell: (84.36, 94.24, 133, 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 1759 8.00 N 1646 7.00 C 6381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 52.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.751A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 removed outlier: 3.740A pdb=" N ILE A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.848A pdb=" N ALA A 141 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN A 142 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 Processing helix chain 'A' and resid 179 through 198 removed outlier: 3.619A pdb=" N ASN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.749A pdb=" N MET A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.581A pdb=" N ILE A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 23 through 34 removed outlier: 3.732A pdb=" N SER B 34 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.617A pdb=" N THR B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 91 removed outlier: 4.420A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Proline residue: B 85 - end of helix Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 149 through 162 removed outlier: 3.566A pdb=" N VAL B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.724A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.889A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.742A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 221 through 229 removed outlier: 4.316A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 3.693A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 279 removed outlier: 3.632A pdb=" N GLY B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 30 Proline residue: C 21 - end of helix removed outlier: 3.913A pdb=" N PHE C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.659A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 88 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 127 through 152 Proline residue: C 141 - end of helix removed outlier: 3.972A pdb=" N LYS C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 166 removed outlier: 4.210A pdb=" N GLU C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.902A pdb=" N LEU C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 197 Proline residue: C 183 - end of helix Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.909A pdb=" N LYS C 223 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 253 Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.602A pdb=" N ARG D 89 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 removed outlier: 4.781A pdb=" N GLY D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET D 116 " --> pdb=" O PHE D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 135 removed outlier: 3.797A pdb=" N ILE D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 3.636A pdb=" N VAL D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.549A pdb=" N GLN D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.569A pdb=" N ALA D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 Processing helix chain 'D' and resid 243 through 248 removed outlier: 3.565A pdb=" N ILE D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.740A pdb=" N LEU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 7.020A pdb=" N LYS A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 7.020A pdb=" N LYS A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 23 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER A 71 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.683A pdb=" N ASN A 92 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ASP A 172 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 94 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 218 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A 229 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 220 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 278 removed outlier: 6.586A pdb=" N ARG A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 260 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN A 270 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 302 removed outlier: 3.989A pdb=" N ALA A 361 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 313 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL A 330 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A 320 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU A 328 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR A 322 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 40 removed outlier: 6.918A pdb=" N LYS D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE D 23 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU D 36 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA D 21 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 38 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN D 19 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 20 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET D 75 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY D 22 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG D 73 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 71 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.561A pdb=" N ILE D 218 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP D 229 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 220 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 276 through 279 removed outlier: 3.735A pdb=" N CYS D 276 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 269 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ARG D 266 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG D 261 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ARG D 268 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE D 259 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 257 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AB1, first strand: chain 'D' and resid 326 through 329 493 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1608 1.32 - 1.44: 2538 1.44 - 1.57: 5783 1.57 - 1.70: 1 1.70 - 1.82: 111 Bond restraints: 10041 Sorted by residual: bond pdb=" CA GLU D 347 " pdb=" C GLU D 347 " ideal model delta sigma weight residual 1.526 1.408 0.118 1.07e-02 8.73e+03 1.22e+02 bond pdb=" N GLU D 347 " pdb=" CA GLU D 347 " ideal model delta sigma weight residual 1.463 1.412 0.051 1.08e-02 8.57e+03 2.27e+01 bond pdb=" C GLU D 347 " pdb=" O GLU D 347 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.03e-02 9.43e+03 1.91e+01 bond pdb=" CA GLU D 347 " pdb=" CB GLU D 347 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.28e-02 6.10e+03 1.21e+01 bond pdb=" C ASN D 346 " pdb=" N GLU D 347 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.24e-02 6.50e+03 7.72e+00 ... (remaining 10036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 13452 2.57 - 5.13: 141 5.13 - 7.70: 19 7.70 - 10.27: 3 10.27 - 12.84: 1 Bond angle restraints: 13616 Sorted by residual: angle pdb=" CB MET D 129 " pdb=" CG MET D 129 " pdb=" SD MET D 129 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C PHE A 352 " pdb=" N ASP A 353 " pdb=" CA ASP A 353 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" CA ASP D 353 " pdb=" C ASP D 353 " pdb=" N HIS D 354 " ideal model delta sigma weight residual 116.84 110.19 6.65 1.71e+00 3.42e-01 1.51e+01 angle pdb=" C ASP D 349 " pdb=" N PRO D 350 " pdb=" CA PRO D 350 " ideal model delta sigma weight residual 119.56 123.38 -3.82 1.01e+00 9.80e-01 1.43e+01 angle pdb=" N ASN D 346 " pdb=" CA ASN D 346 " pdb=" C ASN D 346 " ideal model delta sigma weight residual 108.73 102.59 6.14 1.63e+00 3.76e-01 1.42e+01 ... (remaining 13611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5058 17.30 - 34.60: 698 34.60 - 51.90: 244 51.90 - 69.20: 42 69.20 - 86.49: 8 Dihedral angle restraints: 6050 sinusoidal: 2450 harmonic: 3600 Sorted by residual: dihedral pdb=" N ASP D 353 " pdb=" C ASP D 353 " pdb=" CA ASP D 353 " pdb=" CB ASP D 353 " ideal model delta harmonic sigma weight residual 122.80 143.17 -20.37 0 2.50e+00 1.60e-01 6.64e+01 dihedral pdb=" C ASP D 353 " pdb=" N ASP D 353 " pdb=" CA ASP D 353 " pdb=" CB ASP D 353 " ideal model delta harmonic sigma weight residual -122.60 -142.81 20.21 0 2.50e+00 1.60e-01 6.54e+01 dihedral pdb=" CA ASP A 353 " pdb=" C ASP A 353 " pdb=" N HIS A 354 " pdb=" CA HIS A 354 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 6047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 1594 0.177 - 0.354: 2 0.354 - 0.530: 0 0.530 - 0.707: 0 0.707 - 0.884: 1 Chirality restraints: 1597 Sorted by residual: chirality pdb=" CA ASP D 353 " pdb=" N ASP D 353 " pdb=" C ASP D 353 " pdb=" CB ASP D 353 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" CA PRO A 350 " pdb=" N PRO A 350 " pdb=" C PRO A 350 " pdb=" CB PRO A 350 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN D 346 " pdb=" N ASN D 346 " pdb=" C ASN D 346 " pdb=" CB ASN D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1594 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 349 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 350 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 178 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO C 179 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 231 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 232 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.029 5.00e-02 4.00e+02 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2061 2.78 - 3.31: 8744 3.31 - 3.84: 15359 3.84 - 4.37: 16525 4.37 - 4.90: 30574 Nonbonded interactions: 73263 Sorted by model distance: nonbonded pdb=" O ILE B 146 " pdb=" OG1 THR B 149 " model vdw 2.255 3.040 nonbonded pdb=" OG SER D 149 " pdb=" OE1 GLN D 152 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU D 303 " pdb=" OG SER D 355 " model vdw 2.263 3.040 nonbonded pdb=" O ASP D 306 " pdb=" NE2 GLN D 358 " model vdw 2.289 3.120 nonbonded pdb=" OE1 GLU A 108 " pdb=" NH1 ARG A 115 " model vdw 2.307 3.120 ... (remaining 73258 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 373) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.070 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 0.118 10041 Z= 0.227 Angle : 0.664 12.836 13616 Z= 0.351 Chirality : 0.048 0.884 1597 Planarity : 0.006 0.102 1723 Dihedral : 17.957 86.494 3718 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.30 % Favored : 95.45 % Rotamer: Outliers : 1.84 % Allowed : 31.52 % Favored : 66.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1232 helix: 2.02 (0.23), residues: 574 sheet: 0.60 (0.41), residues: 189 loop : -1.64 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 364 HIS 0.007 0.001 HIS A 146 PHE 0.026 0.001 PHE A 27 TYR 0.008 0.001 TYR A 322 ARG 0.011 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.7870 (pt0) cc_final: 0.7362 (pt0) REVERT: A 186 MET cc_start: 0.7921 (mtm) cc_final: 0.7663 (mtm) REVERT: A 242 LEU cc_start: 0.7976 (mm) cc_final: 0.7740 (mt) REVERT: B 104 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 270 VAL cc_start: 0.7562 (t) cc_final: 0.7316 (t) REVERT: C 99 MET cc_start: 0.6614 (tpt) cc_final: 0.5891 (mtp) REVERT: D 164 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8231 (m110) REVERT: D 297 GLU cc_start: 0.8173 (pm20) cc_final: 0.7920 (pm20) outliers start: 20 outliers final: 14 residues processed: 247 average time/residue: 0.2593 time to fit residues: 86.0541 Evaluate side-chains 244 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 349 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 206 HIS D 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114327 restraints weight = 13356.692| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.17 r_work: 0.3347 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10041 Z= 0.239 Angle : 0.610 8.991 13616 Z= 0.310 Chirality : 0.044 0.224 1597 Planarity : 0.006 0.091 1723 Dihedral : 5.645 51.518 1366 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.89 % Rotamer: Outliers : 4.79 % Allowed : 25.71 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1232 helix: 2.00 (0.22), residues: 589 sheet: 0.32 (0.40), residues: 199 loop : -1.70 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 364 HIS 0.007 0.001 HIS A 146 PHE 0.022 0.001 PHE C 138 TYR 0.010 0.001 TYR D 322 ARG 0.008 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8191 (pt0) cc_final: 0.7658 (pt0) REVERT: A 242 LEU cc_start: 0.8143 (mm) cc_final: 0.7923 (mt) REVERT: A 300 ARG cc_start: 0.7166 (mpt180) cc_final: 0.6701 (mpt180) REVERT: B 270 VAL cc_start: 0.8153 (t) cc_final: 0.7886 (t) REVERT: C 99 MET cc_start: 0.7286 (tpt) cc_final: 0.6283 (mtp) REVERT: D 75 MET cc_start: 0.8004 (mtt) cc_final: 0.7646 (mtt) REVERT: D 88 ASN cc_start: 0.8348 (m-40) cc_final: 0.8142 (m110) REVERT: D 91 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8425 (m) REVERT: D 227 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7725 (mm-30) REVERT: D 360 MET cc_start: 0.3427 (mtm) cc_final: 0.2995 (mtm) REVERT: D 362 ILE cc_start: 0.7608 (pt) cc_final: 0.7198 (mm) outliers start: 52 outliers final: 28 residues processed: 273 average time/residue: 0.2212 time to fit residues: 83.0222 Evaluate side-chains 259 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN D 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114368 restraints weight = 13460.939| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.18 r_work: 0.3347 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10041 Z= 0.202 Angle : 0.568 8.256 13616 Z= 0.289 Chirality : 0.043 0.218 1597 Planarity : 0.006 0.079 1723 Dihedral : 5.017 50.828 1349 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 4.42 % Allowed : 26.27 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1232 helix: 2.10 (0.22), residues: 589 sheet: 0.37 (0.40), residues: 196 loop : -1.66 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.019 0.001 PHE C 138 TYR 0.009 0.001 TYR D 322 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.975 Fit side-chains REVERT: A 60 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 242 LEU cc_start: 0.8159 (mm) cc_final: 0.7941 (mt) REVERT: A 250 GLU cc_start: 0.7749 (mp0) cc_final: 0.7534 (mp0) REVERT: A 300 ARG cc_start: 0.7203 (mpt180) cc_final: 0.6741 (mpt180) REVERT: B 270 VAL cc_start: 0.8127 (t) cc_final: 0.7882 (t) REVERT: C 99 MET cc_start: 0.7315 (tpt) cc_final: 0.6353 (mtp) REVERT: D 91 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8398 (m) REVERT: D 360 MET cc_start: 0.4252 (mtm) cc_final: 0.3940 (mtm) outliers start: 48 outliers final: 28 residues processed: 259 average time/residue: 0.2342 time to fit residues: 81.8914 Evaluate side-chains 259 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 349 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112549 restraints weight = 13376.830| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.19 r_work: 0.3270 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 10041 Z= 0.466 Angle : 0.692 11.119 13616 Z= 0.349 Chirality : 0.049 0.221 1597 Planarity : 0.006 0.067 1723 Dihedral : 5.155 39.320 1347 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.40 % Rotamer: Outliers : 5.35 % Allowed : 24.70 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1232 helix: 1.62 (0.22), residues: 595 sheet: 0.55 (0.41), residues: 183 loop : -1.87 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 364 HIS 0.007 0.002 HIS A 146 PHE 0.028 0.002 PHE C 138 TYR 0.018 0.002 TYR C 17 ARG 0.006 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 1.097 Fit side-chains REVERT: A 44 GLU cc_start: 0.8412 (pt0) cc_final: 0.7986 (pt0) REVERT: A 237 GLU cc_start: 0.7958 (mp0) cc_final: 0.6837 (mp0) REVERT: A 242 LEU cc_start: 0.8163 (mm) cc_final: 0.7941 (mt) REVERT: A 250 GLU cc_start: 0.7769 (mp0) cc_final: 0.7556 (mp0) REVERT: A 300 ARG cc_start: 0.7248 (mpt180) cc_final: 0.6737 (mpt180) REVERT: C 182 MET cc_start: 0.7409 (tpp) cc_final: 0.7086 (tpp) REVERT: D 38 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8241 (tp) REVERT: D 91 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8382 (m) REVERT: D 260 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5779 (pm20) REVERT: D 323 LYS cc_start: 0.8503 (mttp) cc_final: 0.8212 (mttp) REVERT: D 353 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5886 (m-30) REVERT: D 360 MET cc_start: 0.5479 (mtm) cc_final: 0.5278 (mtm) outliers start: 58 outliers final: 37 residues processed: 282 average time/residue: 0.2218 time to fit residues: 86.1477 Evaluate side-chains 278 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN D 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112930 restraints weight = 13458.195| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.16 r_work: 0.3326 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10041 Z= 0.206 Angle : 0.569 8.196 13616 Z= 0.290 Chirality : 0.043 0.144 1597 Planarity : 0.005 0.054 1723 Dihedral : 4.613 36.110 1342 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 4.52 % Allowed : 26.27 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1232 helix: 1.92 (0.22), residues: 595 sheet: 0.30 (0.40), residues: 196 loop : -1.78 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.020 0.001 PHE C 138 TYR 0.008 0.001 TYR D 322 ARG 0.007 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.145 Fit side-chains REVERT: A 44 GLU cc_start: 0.8337 (pt0) cc_final: 0.7793 (pt0) REVERT: A 62 LEU cc_start: 0.8133 (mt) cc_final: 0.7836 (mp) REVERT: A 73 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6849 (mtm110) REVERT: A 75 MET cc_start: 0.7363 (mpp) cc_final: 0.7134 (mpp) REVERT: A 242 LEU cc_start: 0.8154 (mm) cc_final: 0.7928 (mt) REVERT: A 250 GLU cc_start: 0.7733 (mp0) cc_final: 0.7473 (mp0) REVERT: A 300 ARG cc_start: 0.7175 (mpt180) cc_final: 0.6701 (mpt180) REVERT: B 204 MET cc_start: 0.7988 (tpp) cc_final: 0.7587 (tpp) REVERT: B 270 VAL cc_start: 0.8155 (t) cc_final: 0.7920 (t) REVERT: C 99 MET cc_start: 0.7410 (tpt) cc_final: 0.7209 (tpt) REVERT: C 105 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7604 (mmt) REVERT: C 182 MET cc_start: 0.7206 (tpp) cc_final: 0.6843 (mpp) REVERT: C 244 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6743 (ttm) REVERT: D 38 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8212 (tp) REVERT: D 91 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8406 (m) REVERT: D 260 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5669 (pm20) REVERT: D 323 LYS cc_start: 0.8493 (mttp) cc_final: 0.8198 (mttp) REVERT: D 353 ASP cc_start: 0.6191 (OUTLIER) cc_final: 0.5845 (m-30) outliers start: 49 outliers final: 30 residues processed: 261 average time/residue: 0.2468 time to fit residues: 86.8678 Evaluate side-chains 269 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 78 optimal weight: 5.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113846 restraints weight = 13559.928| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.21 r_work: 0.3285 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10041 Z= 0.347 Angle : 0.628 10.241 13616 Z= 0.319 Chirality : 0.046 0.151 1597 Planarity : 0.006 0.056 1723 Dihedral : 4.731 35.426 1342 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 5.07 % Allowed : 25.07 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1232 helix: 1.76 (0.22), residues: 596 sheet: 0.29 (0.40), residues: 194 loop : -1.80 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 364 HIS 0.007 0.001 HIS A 146 PHE 0.024 0.002 PHE C 138 TYR 0.013 0.001 TYR C 17 ARG 0.007 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8440 (pt0) cc_final: 0.7793 (pt0) REVERT: A 237 GLU cc_start: 0.7929 (mp0) cc_final: 0.6714 (mp0) REVERT: A 242 LEU cc_start: 0.8166 (mm) cc_final: 0.7939 (mt) REVERT: A 250 GLU cc_start: 0.7777 (mp0) cc_final: 0.7514 (mp0) REVERT: A 300 ARG cc_start: 0.7256 (mpt180) cc_final: 0.6717 (mpt180) REVERT: C 99 MET cc_start: 0.7452 (tpt) cc_final: 0.7241 (tpt) REVERT: C 105 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7829 (mmt) REVERT: C 178 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7468 (mp) REVERT: C 182 MET cc_start: 0.7360 (tpp) cc_final: 0.7008 (tpp) REVERT: D 32 VAL cc_start: 0.7698 (m) cc_final: 0.7493 (t) REVERT: D 91 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8425 (m) REVERT: D 123 GLU cc_start: 0.8102 (pt0) cc_final: 0.7882 (pt0) REVERT: D 260 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5752 (pm20) REVERT: D 323 LYS cc_start: 0.8544 (mttp) cc_final: 0.8281 (mttp) REVERT: D 353 ASP cc_start: 0.6201 (OUTLIER) cc_final: 0.5880 (m-30) outliers start: 55 outliers final: 37 residues processed: 283 average time/residue: 0.2267 time to fit residues: 87.7700 Evaluate side-chains 286 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN D 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110664 restraints weight = 13909.569| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.28 r_work: 0.3281 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10041 Z= 0.239 Angle : 0.590 9.183 13616 Z= 0.300 Chirality : 0.044 0.148 1597 Planarity : 0.006 0.054 1723 Dihedral : 4.636 35.773 1342 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 4.70 % Allowed : 25.81 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1232 helix: 1.89 (0.22), residues: 595 sheet: 0.29 (0.40), residues: 194 loop : -1.79 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.021 0.001 PHE C 138 TYR 0.009 0.001 TYR D 322 ARG 0.005 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8473 (pt0) cc_final: 0.7854 (pt0) REVERT: A 62 LEU cc_start: 0.8041 (mt) cc_final: 0.7703 (mp) REVERT: A 242 LEU cc_start: 0.8087 (mm) cc_final: 0.7870 (mt) REVERT: A 250 GLU cc_start: 0.7747 (mp0) cc_final: 0.7447 (mp0) REVERT: A 300 ARG cc_start: 0.7215 (mpt180) cc_final: 0.6599 (mpt180) REVERT: B 204 MET cc_start: 0.7967 (tpp) cc_final: 0.7520 (tpp) REVERT: B 270 VAL cc_start: 0.7927 (t) cc_final: 0.7691 (t) REVERT: C 105 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7696 (mmt) REVERT: C 178 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7315 (mp) REVERT: C 182 MET cc_start: 0.7245 (tpp) cc_final: 0.6992 (tpp) REVERT: D 91 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (m) REVERT: D 260 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5799 (pm20) REVERT: D 323 LYS cc_start: 0.8519 (mttp) cc_final: 0.8233 (mttp) REVERT: D 353 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5754 (m-30) outliers start: 51 outliers final: 37 residues processed: 272 average time/residue: 0.2274 time to fit residues: 84.5133 Evaluate side-chains 285 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110949 restraints weight = 13813.944| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.27 r_work: 0.3285 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10041 Z= 0.235 Angle : 0.590 9.225 13616 Z= 0.299 Chirality : 0.044 0.146 1597 Planarity : 0.006 0.058 1723 Dihedral : 4.587 36.134 1342 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 4.52 % Allowed : 25.90 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1232 helix: 1.96 (0.22), residues: 595 sheet: 0.23 (0.40), residues: 196 loop : -1.79 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.022 0.001 PHE C 138 TYR 0.016 0.001 TYR C 148 ARG 0.006 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8477 (pt0) cc_final: 0.8165 (pt0) REVERT: A 62 LEU cc_start: 0.8030 (mt) cc_final: 0.7705 (mp) REVERT: A 242 LEU cc_start: 0.8091 (mm) cc_final: 0.7872 (mt) REVERT: A 250 GLU cc_start: 0.7750 (mp0) cc_final: 0.7436 (mp0) REVERT: A 300 ARG cc_start: 0.7198 (mpt180) cc_final: 0.6582 (mpt180) REVERT: B 204 MET cc_start: 0.7959 (tpp) cc_final: 0.7462 (tpp) REVERT: B 270 VAL cc_start: 0.7907 (t) cc_final: 0.7667 (t) REVERT: C 105 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7759 (mmt) REVERT: C 178 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7268 (mp) REVERT: C 182 MET cc_start: 0.7244 (tpp) cc_final: 0.6983 (tpp) REVERT: D 91 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8417 (m) REVERT: D 169 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7968 (tp) REVERT: D 260 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5800 (pm20) REVERT: D 323 LYS cc_start: 0.8525 (mttp) cc_final: 0.8253 (mttp) REVERT: D 353 ASP cc_start: 0.5931 (OUTLIER) cc_final: 0.5615 (m-30) outliers start: 49 outliers final: 38 residues processed: 268 average time/residue: 0.2333 time to fit residues: 85.3089 Evaluate side-chains 280 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN D 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110848 restraints weight = 13852.242| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.25 r_work: 0.3287 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10041 Z= 0.237 Angle : 0.596 9.431 13616 Z= 0.301 Chirality : 0.044 0.144 1597 Planarity : 0.006 0.060 1723 Dihedral : 4.571 36.257 1342 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 4.33 % Allowed : 26.36 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1232 helix: 1.95 (0.22), residues: 595 sheet: 0.29 (0.40), residues: 194 loop : -1.72 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.022 0.001 PHE C 138 TYR 0.018 0.001 TYR C 148 ARG 0.007 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8475 (pt0) cc_final: 0.8158 (pt0) REVERT: A 62 LEU cc_start: 0.8021 (mt) cc_final: 0.7693 (mp) REVERT: A 214 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7772 (ptp) REVERT: A 242 LEU cc_start: 0.8083 (mm) cc_final: 0.7865 (mt) REVERT: A 250 GLU cc_start: 0.7753 (mp0) cc_final: 0.7446 (mp0) REVERT: A 300 ARG cc_start: 0.7215 (mpt180) cc_final: 0.6597 (mpt180) REVERT: A 360 MET cc_start: 0.5181 (mpp) cc_final: 0.4869 (mpp) REVERT: B 204 MET cc_start: 0.7938 (tpp) cc_final: 0.7421 (tpp) REVERT: B 270 VAL cc_start: 0.7882 (t) cc_final: 0.7636 (t) REVERT: C 99 MET cc_start: 0.7320 (tpt) cc_final: 0.6422 (mtm) REVERT: C 178 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7254 (mp) REVERT: C 182 MET cc_start: 0.7218 (tpp) cc_final: 0.6954 (tpp) REVERT: D 91 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8413 (m) REVERT: D 169 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7970 (tp) REVERT: D 260 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5796 (pm20) REVERT: D 353 ASP cc_start: 0.5697 (OUTLIER) cc_final: 0.5361 (m-30) outliers start: 47 outliers final: 35 residues processed: 262 average time/residue: 0.2336 time to fit residues: 83.2387 Evaluate side-chains 273 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112129 restraints weight = 13737.287| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.25 r_work: 0.3304 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10041 Z= 0.192 Angle : 0.580 8.717 13616 Z= 0.292 Chirality : 0.043 0.137 1597 Planarity : 0.005 0.060 1723 Dihedral : 4.455 36.801 1342 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 3.13 % Allowed : 27.74 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1232 helix: 2.02 (0.22), residues: 597 sheet: 0.23 (0.39), residues: 196 loop : -1.68 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.020 0.001 PHE C 138 TYR 0.013 0.001 TYR C 148 ARG 0.007 0.000 ARG A 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8441 (pt0) cc_final: 0.8115 (pt0) REVERT: A 62 LEU cc_start: 0.8021 (mt) cc_final: 0.7721 (mp) REVERT: A 237 GLU cc_start: 0.7952 (mp0) cc_final: 0.6593 (mp0) REVERT: A 242 LEU cc_start: 0.8060 (mm) cc_final: 0.7848 (mt) REVERT: A 250 GLU cc_start: 0.7754 (mp0) cc_final: 0.7442 (mp0) REVERT: A 297 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 300 ARG cc_start: 0.7192 (mpt180) cc_final: 0.6580 (mpt180) REVERT: B 204 MET cc_start: 0.7856 (tpp) cc_final: 0.7394 (tpp) REVERT: B 208 ILE cc_start: 0.8050 (mm) cc_final: 0.7785 (mt) REVERT: B 270 VAL cc_start: 0.7832 (t) cc_final: 0.7607 (t) REVERT: C 99 MET cc_start: 0.7381 (tpt) cc_final: 0.6440 (mtm) REVERT: C 182 MET cc_start: 0.7190 (tpp) cc_final: 0.6938 (tpp) REVERT: D 91 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8421 (m) REVERT: D 260 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5706 (pm20) REVERT: D 353 ASP cc_start: 0.5508 (OUTLIER) cc_final: 0.5236 (m-30) outliers start: 34 outliers final: 26 residues processed: 250 average time/residue: 0.2348 time to fit residues: 79.3338 Evaluate side-chains 255 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 95 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113179 restraints weight = 13829.762| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.26 r_work: 0.3320 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10041 Z= 0.172 Angle : 0.576 8.351 13616 Z= 0.289 Chirality : 0.043 0.123 1597 Planarity : 0.005 0.060 1723 Dihedral : 4.405 37.483 1342 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 3.23 % Allowed : 27.74 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1232 helix: 2.10 (0.22), residues: 594 sheet: 0.28 (0.40), residues: 195 loop : -1.64 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.018 0.001 PHE C 138 TYR 0.007 0.001 TYR B 223 ARG 0.007 0.000 ARG A 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.28 seconds wall clock time: 93 minutes 57.80 seconds (5637.80 seconds total)