Starting phenix.real_space_refine on Thu Jan 16 16:02:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5f_38933/01_2025/8y5f_38933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5f_38933/01_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_38933/01_2025/8y5f_38933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5f_38933/01_2025/8y5f_38933.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5f_38933/01_2025/8y5f_38933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5f_38933/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.76, per 1000 atoms: 0.59 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 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: 1.07 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: 2.89 Time building geometry restraints manager: 2.84 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.580 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: 0.010 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: 29.690 ------------------------------------------------------------------------------- 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 : 1.039 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: 0.2484 time to fit residues: 82.4408 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 : 1.209 ------------------------------------------------------------------------------- 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 = 0.114328 restraints weight = 13356.694| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.17 r_work: 0.3346 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 : 1.142 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8192 (pt0) cc_final: 0.7659 (pt0) REVERT: A 242 LEU cc_start: 0.8144 (mm) cc_final: 0.7924 (mt) REVERT: A 300 ARG cc_start: 0.7174 (mpt180) cc_final: 0.6712 (mpt180) REVERT: B 270 VAL cc_start: 0.8144 (t) cc_final: 0.7877 (t) REVERT: C 99 MET cc_start: 0.7287 (tpt) cc_final: 0.6283 (mtp) REVERT: D 75 MET cc_start: 0.8005 (mtt) cc_final: 0.7646 (mtt) REVERT: D 88 ASN cc_start: 0.8347 (m-40) cc_final: 0.8142 (m110) REVERT: D 91 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8425 (m) REVERT: D 227 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7725 (mm-30) REVERT: D 360 MET cc_start: 0.3445 (mtm) cc_final: 0.3015 (mtm) REVERT: D 362 ILE cc_start: 0.7613 (pt) cc_final: 0.7202 (mm) outliers start: 52 outliers final: 28 residues processed: 273 average time/residue: 0.2314 time to fit residues: 86.8346 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 : 1.220 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.9990 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.135414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114160 restraints weight = 13454.776| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.19 r_work: 0.3344 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1263 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= 0.209 Angle : 0.572 8.375 13616 Z= 0.291 Chirality : 0.043 0.220 1597 Planarity : 0.006 0.079 1723 Dihedral : 5.029 51.003 1349 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 4.52 % Allowed : 26.18 % 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: 0.76 (0.25), residues: 1232 helix: 2.08 (0.22), residues: 590 sheet: 0.35 (0.40), residues: 197 loop : -1.67 (0.28), residues: 445 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 0.020 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 282 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.853 Fit side-chains REVERT: A 60 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7466 (mp) REVERT: A 242 LEU cc_start: 0.8160 (mm) cc_final: 0.7942 (mt) REVERT: A 250 GLU cc_start: 0.7752 (mp0) cc_final: 0.7536 (mp0) REVERT: A 300 ARG cc_start: 0.7193 (mpt180) cc_final: 0.6730 (mpt180) REVERT: B 270 VAL cc_start: 0.8123 (t) cc_final: 0.7879 (t) REVERT: C 99 MET cc_start: 0.7319 (tpt) cc_final: 0.6361 (mtp) REVERT: D 91 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8432 (m) REVERT: D 360 MET cc_start: 0.4271 (mtm) cc_final: 0.3970 (mtm) outliers start: 49 outliers final: 28 residues processed: 262 average time/residue: 0.2479 time to fit residues: 87.5995 Evaluate side-chains 261 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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: 4.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.9444 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.134270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113432 restraints weight = 13363.877| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.20 r_work: 0.3284 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10041 Z= 0.376 Angle : 0.656 10.975 13616 Z= 0.331 Chirality : 0.047 0.215 1597 Planarity : 0.006 0.067 1723 Dihedral : 5.035 38.418 1347 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.19 % Favored : 94.64 % Rotamer: Outliers : 5.44 % Allowed : 24.61 % 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: 0.46 (0.25), residues: 1232 helix: 1.73 (0.22), residues: 596 sheet: 0.58 (0.42), residues: 183 loop : -1.83 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 364 HIS 0.007 0.001 HIS A 146 PHE 0.027 0.002 PHE C 138 TYR 0.015 0.002 TYR C 17 ARG 0.005 0.000 ARG D 73 *********************** 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 297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 1.185 Fit side-chains REVERT: A 44 GLU cc_start: 0.8387 (pt0) cc_final: 0.7746 (pt0) REVERT: A 237 GLU cc_start: 0.7934 (mp0) cc_final: 0.6820 (mp0) REVERT: A 242 LEU cc_start: 0.8165 (mm) cc_final: 0.7940 (mt) REVERT: A 250 GLU cc_start: 0.7777 (mp0) cc_final: 0.7561 (mp0) REVERT: A 300 ARG cc_start: 0.7211 (mpt180) cc_final: 0.6705 (mpt180) REVERT: C 149 SER cc_start: 0.8530 (p) cc_final: 0.8328 (m) REVERT: C 182 MET cc_start: 0.7372 (tpp) cc_final: 0.7027 (tpp) REVERT: D 38 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8230 (tp) REVERT: D 91 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8382 (m) REVERT: D 260 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5772 (pm20) REVERT: D 277 ASN cc_start: 0.8193 (p0) cc_final: 0.7969 (p0) REVERT: D 323 LYS cc_start: 0.8502 (mttp) cc_final: 0.8187 (mttp) REVERT: D 353 ASP cc_start: 0.6219 (OUTLIER) cc_final: 0.5821 (m-30) REVERT: D 360 MET cc_start: 0.5387 (mtm) cc_final: 0.5184 (mtm) outliers start: 59 outliers final: 36 residues processed: 274 average time/residue: 0.2393 time to fit residues: 89.8516 Evaluate side-chains 275 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain A residue 234 GLU 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 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 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: 1.9990 chunk 8 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 40 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 chunk 38 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.135040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113996 restraints weight = 13453.520| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.17 r_work: 0.3342 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10041 Z= 0.174 Angle : 0.555 8.121 13616 Z= 0.283 Chirality : 0.043 0.143 1597 Planarity : 0.005 0.053 1723 Dihedral : 4.515 36.349 1342 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 3.96 % Allowed : 26.45 % 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: 0.70 (0.25), residues: 1232 helix: 2.00 (0.22), residues: 596 sheet: 0.36 (0.40), residues: 195 loop : -1.72 (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 0.019 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: 43 poor density : 237 time to evaluate : 1.142 Fit side-chains REVERT: A 62 LEU cc_start: 0.8136 (mt) cc_final: 0.7832 (mp) REVERT: A 242 LEU cc_start: 0.8155 (mm) cc_final: 0.7932 (mt) REVERT: A 250 GLU cc_start: 0.7738 (mp0) cc_final: 0.7472 (mp0) REVERT: A 300 ARG cc_start: 0.7190 (mpt180) cc_final: 0.6718 (mpt180) REVERT: B 204 MET cc_start: 0.7953 (tpp) cc_final: 0.7593 (tpp) REVERT: B 270 VAL cc_start: 0.8165 (t) cc_final: 0.7880 (t) REVERT: C 149 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8277 (m) REVERT: C 182 MET cc_start: 0.7162 (tpp) cc_final: 0.6792 (mpp) REVERT: C 244 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6726 (ttm) REVERT: D 38 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8193 (tp) REVERT: D 89 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7666 (mtt180) REVERT: D 91 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8413 (m) REVERT: D 260 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5640 (pm20) REVERT: D 323 LYS cc_start: 0.8456 (mttp) cc_final: 0.8126 (mttp) REVERT: D 353 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5721 (m-30) outliers start: 43 outliers final: 29 residues processed: 265 average time/residue: 0.2628 time to fit residues: 92.5301 Evaluate side-chains 272 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 VAL 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 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 36 LEU 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 C residue 18 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 149 SER 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 60 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 260 GLU 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: 1.9990 chunk 3 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.134218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113287 restraints weight = 13559.079| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.22 r_work: 0.3281 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10041 Z= 0.359 Angle : 0.644 10.614 13616 Z= 0.324 Chirality : 0.047 0.154 1597 Planarity : 0.006 0.055 1723 Dihedral : 4.719 35.416 1342 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % 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: 0.50 (0.25), residues: 1232 helix: 1.78 (0.22), residues: 594 sheet: 0.36 (0.40), residues: 193 loop : -1.75 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 364 HIS 0.007 0.001 HIS A 146 PHE 0.025 0.002 PHE C 138 TYR 0.014 0.002 TYR C 17 ARG 0.007 0.001 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 300 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.017 Fit side-chains REVERT: A 44 GLU cc_start: 0.8370 (pt0) cc_final: 0.7711 (pt0) REVERT: A 237 GLU cc_start: 0.7937 (mp0) cc_final: 0.6790 (mp0) REVERT: A 242 LEU cc_start: 0.8193 (mm) cc_final: 0.7963 (mt) REVERT: A 250 GLU cc_start: 0.7783 (mp0) cc_final: 0.7524 (mp0) REVERT: A 300 ARG cc_start: 0.7251 (mpt180) cc_final: 0.6718 (mpt180) REVERT: C 99 MET cc_start: 0.7316 (tpt) cc_final: 0.6394 (mtp) REVERT: C 149 SER cc_start: 0.8602 (p) cc_final: 0.8379 (m) REVERT: C 182 MET cc_start: 0.7389 (tpp) cc_final: 0.7060 (tpp) REVERT: D 38 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8224 (tp) REVERT: D 91 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8425 (m) REVERT: D 123 GLU cc_start: 0.8086 (pt0) cc_final: 0.7850 (pt0) REVERT: D 260 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5769 (pm20) REVERT: D 277 ASN cc_start: 0.8236 (p0) cc_final: 0.7967 (p0) REVERT: D 323 LYS cc_start: 0.8530 (mttp) cc_final: 0.8225 (mttp) REVERT: D 353 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5804 (m-30) outliers start: 55 outliers final: 39 residues processed: 278 average time/residue: 0.2410 time to fit residues: 90.6688 Evaluate side-chains 281 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 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 64 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 18 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 173 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 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 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 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: 2.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 78 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.132147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110636 restraints weight = 13907.474| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.28 r_work: 0.3280 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10041 Z= 0.244 Angle : 0.600 9.247 13616 Z= 0.303 Chirality : 0.044 0.156 1597 Planarity : 0.005 0.054 1723 Dihedral : 4.619 35.797 1342 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 5.16 % Allowed : 25.53 % 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: 0.57 (0.25), residues: 1232 helix: 1.87 (0.22), residues: 595 sheet: 0.34 (0.40), residues: 194 loop : -1.77 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 364 HIS 0.008 0.001 HIS A 146 PHE 0.022 0.001 PHE C 138 TYR 0.009 0.001 TYR D 322 ARG 0.006 0.000 ARG A 167 *********************** 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 292 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8406 (pt0) cc_final: 0.7757 (pt0) REVERT: A 62 LEU cc_start: 0.8023 (mt) cc_final: 0.7699 (mp) REVERT: A 242 LEU cc_start: 0.8080 (mm) cc_final: 0.7862 (mt) REVERT: A 250 GLU cc_start: 0.7724 (mp0) cc_final: 0.7423 (mp0) REVERT: A 300 ARG cc_start: 0.7222 (mpt180) cc_final: 0.6604 (mpt180) REVERT: B 204 MET cc_start: 0.7972 (tpp) cc_final: 0.7491 (tpp) REVERT: B 270 VAL cc_start: 0.7880 (t) cc_final: 0.7663 (t) REVERT: C 99 MET cc_start: 0.7300 (tpt) cc_final: 0.6327 (mtm) REVERT: C 105 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7879 (mmt) REVERT: C 149 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8360 (m) REVERT: C 178 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7302 (mp) REVERT: C 182 MET cc_start: 0.7258 (tpp) cc_final: 0.7001 (tpp) REVERT: D 38 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8107 (tp) REVERT: D 81 ILE cc_start: 0.8454 (mm) cc_final: 0.8218 (mt) REVERT: D 91 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8408 (m) REVERT: D 123 GLU cc_start: 0.8093 (pt0) cc_final: 0.7778 (pt0) REVERT: D 260 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5766 (pm20) REVERT: D 277 ASN cc_start: 0.8142 (p0) cc_final: 0.7827 (p0) REVERT: D 323 LYS cc_start: 0.8501 (mttp) cc_final: 0.8200 (mttp) REVERT: D 353 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5604 (m-30) outliers start: 56 outliers final: 38 residues processed: 270 average time/residue: 0.2361 time to fit residues: 87.2024 Evaluate side-chains 282 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG 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 149 SER 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 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 104 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 163 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: 9.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.133538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112050 restraints weight = 13853.192| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.28 r_work: 0.3302 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10041 Z= 0.189 Angle : 0.582 8.937 13616 Z= 0.291 Chirality : 0.043 0.136 1597 Planarity : 0.005 0.056 1723 Dihedral : 4.452 36.630 1342 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 3.87 % Allowed : 27.10 % 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: 0.71 (0.25), residues: 1232 helix: 2.03 (0.22), residues: 596 sheet: 0.33 (0.40), residues: 195 loop : -1.73 (0.27), residues: 441 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 0.019 0.001 PHE C 138 TYR 0.010 0.001 TYR D 322 ARG 0.004 0.000 ARG D 225 *********************** 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 267 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8356 (pt0) cc_final: 0.7769 (pt0) REVERT: A 62 LEU cc_start: 0.8041 (mt) cc_final: 0.7740 (mp) REVERT: A 242 LEU cc_start: 0.8070 (mm) cc_final: 0.7860 (mt) REVERT: A 250 GLU cc_start: 0.7773 (mp0) cc_final: 0.7465 (mp0) REVERT: A 300 ARG cc_start: 0.7187 (mpt180) cc_final: 0.6573 (mpt180) REVERT: B 204 MET cc_start: 0.7878 (tpp) cc_final: 0.7457 (tpp) REVERT: B 270 VAL cc_start: 0.7876 (t) cc_final: 0.7647 (t) REVERT: C 99 MET cc_start: 0.7316 (tpt) cc_final: 0.6329 (mtm) REVERT: C 149 SER cc_start: 0.8545 (p) cc_final: 0.8339 (m) REVERT: C 182 MET cc_start: 0.7184 (tpp) cc_final: 0.6925 (tpp) REVERT: D 38 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8096 (tp) REVERT: D 81 ILE cc_start: 0.8461 (mm) cc_final: 0.8221 (mt) REVERT: D 91 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8423 (m) REVERT: D 260 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5757 (pm20) REVERT: D 277 ASN cc_start: 0.8145 (p0) cc_final: 0.7827 (p0) REVERT: D 323 LYS cc_start: 0.8492 (mttp) cc_final: 0.8200 (mttp) REVERT: D 353 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.5389 (m-30) outliers start: 42 outliers final: 35 residues processed: 253 average time/residue: 0.2426 time to fit residues: 83.5329 Evaluate side-chains 257 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 38 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 163 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 0.0370 chunk 119 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.0060 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.2232 ------------------------------------------------------------------------------- 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 B 238 ASN D 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115984 restraints weight = 13841.598| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.27 r_work: 0.3356 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10041 Z= 0.144 Angle : 0.557 8.202 13616 Z= 0.277 Chirality : 0.042 0.144 1597 Planarity : 0.005 0.057 1723 Dihedral : 4.240 38.166 1342 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 3.32 % Allowed : 27.28 % Favored : 69.40 % 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: 0.93 (0.25), residues: 1232 helix: 2.22 (0.22), residues: 593 sheet: 0.37 (0.40), residues: 195 loop : -1.57 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 364 HIS 0.009 0.001 HIS A 146 PHE 0.015 0.001 PHE C 138 TYR 0.008 0.001 TYR D 322 ARG 0.005 0.000 ARG D 225 *********************** 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 272 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8026 (mt) cc_final: 0.7701 (mp) REVERT: A 241 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7810 (p0) REVERT: A 242 LEU cc_start: 0.8066 (mm) cc_final: 0.7847 (mt) REVERT: A 250 GLU cc_start: 0.7820 (mp0) cc_final: 0.7460 (mp0) REVERT: A 297 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 300 ARG cc_start: 0.7140 (mpt180) cc_final: 0.6539 (mpt180) REVERT: B 267 MET cc_start: 0.7668 (mtm) cc_final: 0.7416 (mtt) REVERT: B 270 VAL cc_start: 0.7777 (t) cc_final: 0.7522 (t) REVERT: C 99 MET cc_start: 0.7271 (tpt) cc_final: 0.6293 (mtm) REVERT: C 149 SER cc_start: 0.8518 (p) cc_final: 0.8261 (m) REVERT: C 182 MET cc_start: 0.6977 (tpp) cc_final: 0.6770 (tpp) REVERT: D 38 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8022 (tp) REVERT: D 227 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7621 (mm-30) REVERT: D 237 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8023 (mt-10) REVERT: D 260 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5507 (pm20) REVERT: D 297 GLU cc_start: 0.8498 (pm20) cc_final: 0.8218 (pm20) REVERT: D 353 ASP cc_start: 0.5347 (OUTLIER) cc_final: 0.5124 (m-30) outliers start: 36 outliers final: 23 residues processed: 260 average time/residue: 0.2555 time to fit residues: 88.6646 Evaluate side-chains 254 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 241 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 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 197 ARG 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 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 134 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 200 THR 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 91 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.131870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110381 restraints weight = 13821.061| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.29 r_work: 0.3273 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10041 Z= 0.318 Angle : 0.643 10.195 13616 Z= 0.320 Chirality : 0.045 0.216 1597 Planarity : 0.006 0.060 1723 Dihedral : 4.452 37.081 1342 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 3.13 % Allowed : 27.28 % 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: 0.77 (0.25), residues: 1232 helix: 2.01 (0.22), residues: 593 sheet: 0.47 (0.40), residues: 193 loop : -1.60 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 364 HIS 0.008 0.001 HIS A 146 PHE 0.024 0.002 PHE C 138 TYR 0.013 0.001 TYR B 223 ARG 0.015 0.001 ARG A 233 ********************** 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 : 1.048 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8316 (pt0) cc_final: 0.7943 (pt0) REVERT: A 75 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7594 (mpp) REVERT: A 186 MET cc_start: 0.8004 (mtm) cc_final: 0.7801 (mtm) REVERT: A 250 GLU cc_start: 0.7890 (mp0) cc_final: 0.7537 (mp0) REVERT: A 297 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: A 300 ARG cc_start: 0.7200 (mpt180) cc_final: 0.6619 (mpt180) REVERT: A 335 ASN cc_start: 0.7849 (t0) cc_final: 0.7562 (t0) REVERT: B 270 VAL cc_start: 0.7958 (t) cc_final: 0.7735 (t) REVERT: C 99 MET cc_start: 0.7440 (tpt) cc_final: 0.6542 (mtm) REVERT: C 149 SER cc_start: 0.8596 (p) cc_final: 0.8352 (m) REVERT: C 182 MET cc_start: 0.7313 (tpp) cc_final: 0.6931 (mpp) REVERT: D 38 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8167 (tp) REVERT: D 323 LYS cc_start: 0.8519 (mttp) cc_final: 0.8295 (mttp) REVERT: D 353 ASP cc_start: 0.5347 (OUTLIER) cc_final: 0.5085 (m-30) outliers start: 34 outliers final: 25 residues processed: 250 average time/residue: 0.2192 time to fit residues: 76.1824 Evaluate side-chains 264 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 VAL 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 197 ARG Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 18 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 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 134 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 200 THR 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: 3.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.133595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112016 restraints weight = 13912.292| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.30 r_work: 0.3297 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10041 Z= 0.204 Angle : 0.608 9.285 13616 Z= 0.304 Chirality : 0.043 0.155 1597 Planarity : 0.006 0.059 1723 Dihedral : 4.405 37.539 1342 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 3.13 % Allowed : 27.56 % 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: 0.80 (0.25), residues: 1232 helix: 2.05 (0.22), residues: 594 sheet: 0.40 (0.40), residues: 196 loop : -1.60 (0.28), residues: 442 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 0.020 0.001 PHE C 138 TYR 0.010 0.001 TYR D 322 ARG 0.014 0.001 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4992.15 seconds wall clock time: 89 minutes 0.16 seconds (5340.16 seconds total)