Starting phenix.real_space_refine on Wed Sep 17 16:18:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5f_38933/09_2025/8y5f_38933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5f_38933/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y5f_38933/09_2025/8y5f_38933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5f_38933/09_2025/8y5f_38933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y5f_38933/09_2025/8y5f_38933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5f_38933/09_2025/8y5f_38933.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.31, per 1000 atoms: 0.23 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: 0.93 Conformation dependent library (CDL) restraints added in 349.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.34 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: 1.60 Time building geometry restraints manager: 1.22 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: 1.700 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- 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= 0.196 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (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 ARG 0.011 0.001 ARG A 133 TYR 0.008 0.001 TYR A 322 PHE 0.026 0.001 PHE A 27 TRP 0.008 0.001 TRP A 364 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00347 (10041) covalent geometry : angle 0.66371 (13616) hydrogen bonds : bond 0.19212 ( 490) hydrogen bonds : angle 6.35358 ( 1404) *********************** 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 : 0.272 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: 0.1075 time to fit residues: 35.7294 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 : 0.345 ------------------------------------------------------------------------------- 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 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN D 206 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117136 restraints weight = 13510.515| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.19 r_work: 0.3380 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10041 Z= 0.117 Angle : 0.578 8.393 13616 Z= 0.295 Chirality : 0.043 0.223 1597 Planarity : 0.006 0.093 1723 Dihedral : 5.503 49.054 1366 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 4.70 % Allowed : 26.18 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1232 helix: 2.15 (0.22), residues: 588 sheet: 0.40 (0.40), residues: 197 loop : -1.66 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 133 TYR 0.008 0.001 TYR D 322 PHE 0.018 0.001 PHE C 138 TRP 0.010 0.001 TRP D 364 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00264 (10041) covalent geometry : angle 0.57807 (13616) hydrogen bonds : bond 0.04361 ( 490) hydrogen bonds : angle 4.59967 ( 1404) *********************** 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 285 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7175 (mmt90) cc_final: 0.6839 (mtt90) REVERT: A 242 LEU cc_start: 0.8130 (mm) cc_final: 0.7922 (mt) REVERT: A 300 ARG cc_start: 0.7153 (mpt180) cc_final: 0.6709 (mpt180) REVERT: B 29 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7367 (mtp) REVERT: B 270 VAL cc_start: 0.8049 (t) cc_final: 0.7759 (t) REVERT: C 99 MET cc_start: 0.7204 (tpt) cc_final: 0.6232 (mtp) REVERT: D 24 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7535 (tpp80) REVERT: D 91 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8426 (m) REVERT: D 215 SER cc_start: 0.8423 (p) cc_final: 0.8216 (p) REVERT: D 277 ASN cc_start: 0.8143 (p0) cc_final: 0.7928 (p0) REVERT: D 353 ASP cc_start: 0.6358 (OUTLIER) cc_final: 0.5880 (m-30) REVERT: D 360 MET cc_start: 0.3205 (mtm) cc_final: 0.2729 (mtm) outliers start: 51 outliers final: 26 residues processed: 264 average time/residue: 0.0943 time to fit residues: 34.2070 Evaluate side-chains 251 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 214 MET 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 301 VAL Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 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 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 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 58 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 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 = 0.135205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113906 restraints weight = 13494.982| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.19 r_work: 0.3324 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10041 Z= 0.151 Angle : 0.588 9.976 13616 Z= 0.296 Chirality : 0.044 0.220 1597 Planarity : 0.006 0.078 1723 Dihedral : 4.822 40.092 1347 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 4.70 % Allowed : 25.16 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1232 helix: 2.06 (0.22), residues: 591 sheet: 0.43 (0.40), residues: 196 loop : -1.63 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.010 0.001 TYR B 223 PHE 0.020 0.001 PHE C 138 TRP 0.008 0.001 TRP A 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00368 (10041) covalent geometry : angle 0.58843 (13616) hydrogen bonds : bond 0.04960 ( 490) hydrogen bonds : angle 4.40221 ( 1404) *********************** 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 287 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.371 Fit side-chains REVERT: A 214 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7816 (ptp) REVERT: A 242 LEU cc_start: 0.8191 (mm) cc_final: 0.7975 (mt) REVERT: A 300 ARG cc_start: 0.7195 (mpt180) cc_final: 0.6717 (mpt180) REVERT: B 270 VAL cc_start: 0.8098 (t) cc_final: 0.7839 (t) REVERT: D 277 ASN cc_start: 0.8182 (p0) cc_final: 0.7916 (p0) REVERT: D 323 LYS cc_start: 0.8357 (mttp) cc_final: 0.8007 (mttp) REVERT: D 353 ASP cc_start: 0.6154 (OUTLIER) cc_final: 0.5742 (m-30) outliers start: 51 outliers final: 28 residues processed: 264 average time/residue: 0.1062 time to fit residues: 37.9862 Evaluate side-chains 264 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 226 ILE 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 18 LEU Chi-restraints excluded: chain C residue 198 ASP 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 60 LEU Chi-restraints excluded: chain D residue 69 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 294 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112299 restraints weight = 13649.418| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.21 r_work: 0.3269 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 10041 Z= 0.275 Angle : 0.696 11.420 13616 Z= 0.351 Chirality : 0.049 0.213 1597 Planarity : 0.006 0.066 1723 Dihedral : 5.181 38.300 1347 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.40 % Rotamer: Outliers : 5.35 % Allowed : 25.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.24), residues: 1232 helix: 1.59 (0.22), residues: 596 sheet: 0.52 (0.41), residues: 183 loop : -1.84 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 73 TYR 0.018 0.002 TYR C 17 PHE 0.029 0.002 PHE C 138 TRP 0.015 0.002 TRP A 364 HIS 0.007 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00692 (10041) covalent geometry : angle 0.69561 (13616) hydrogen bonds : bond 0.06596 ( 490) hydrogen bonds : angle 4.59753 ( 1404) *********************** 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: 58 poor density : 239 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7950 (mp0) cc_final: 0.6840 (mp0) REVERT: A 242 LEU cc_start: 0.8158 (mm) cc_final: 0.7923 (mt) REVERT: A 300 ARG cc_start: 0.7242 (mpt180) cc_final: 0.6725 (mpt180) REVERT: C 149 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8342 (m) REVERT: C 182 MET cc_start: 0.7441 (tpp) cc_final: 0.7107 (tpp) REVERT: D 38 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8242 (tp) REVERT: D 260 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5806 (pm20) REVERT: D 277 ASN cc_start: 0.8184 (p0) cc_final: 0.7925 (p0) REVERT: D 323 LYS cc_start: 0.8504 (mttp) cc_final: 0.8239 (mttp) REVERT: D 353 ASP cc_start: 0.6294 (OUTLIER) cc_final: 0.5902 (m-30) REVERT: D 360 MET cc_start: 0.5467 (mtm) cc_final: 0.5242 (mtm) outliers start: 58 outliers final: 34 residues processed: 273 average time/residue: 0.0957 time to fit residues: 36.2052 Evaluate side-chains 275 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 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 122 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 173 LEU 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 92 ASN 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 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 70 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112707 restraints weight = 13574.641| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.17 r_work: 0.3304 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10041 Z= 0.134 Angle : 0.575 8.712 13616 Z= 0.293 Chirality : 0.044 0.146 1597 Planarity : 0.005 0.054 1723 Dihedral : 4.637 35.982 1342 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 4.70 % Allowed : 25.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1232 helix: 1.89 (0.22), residues: 595 sheet: 0.32 (0.40), residues: 196 loop : -1.77 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 225 TYR 0.008 0.001 TYR D 322 PHE 0.020 0.001 PHE C 138 TRP 0.009 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00315 (10041) covalent geometry : angle 0.57525 (13616) hydrogen bonds : bond 0.04765 ( 490) hydrogen bonds : angle 4.31720 ( 1404) *********************** 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 289 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.264 Fit side-chains REVERT: A 62 LEU cc_start: 0.8142 (mt) cc_final: 0.7831 (mp) REVERT: A 242 LEU cc_start: 0.8141 (mm) cc_final: 0.7915 (mt) REVERT: A 300 ARG cc_start: 0.7195 (mpt180) cc_final: 0.6702 (mpt180) REVERT: B 270 VAL cc_start: 0.8187 (t) cc_final: 0.7946 (t) REVERT: C 182 MET cc_start: 0.7222 (tpp) cc_final: 0.6859 (mpp) REVERT: D 38 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8198 (tp) REVERT: D 76 LEU cc_start: 0.7696 (mp) cc_final: 0.7436 (mt) REVERT: D 260 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5655 (pm20) REVERT: D 277 ASN cc_start: 0.8220 (p0) cc_final: 0.7851 (p0) REVERT: D 323 LYS cc_start: 0.8506 (mttp) cc_final: 0.8234 (mttp) REVERT: D 353 ASP cc_start: 0.6163 (OUTLIER) cc_final: 0.5779 (m-30) outliers start: 51 outliers final: 39 residues processed: 268 average time/residue: 0.1019 time to fit residues: 37.4636 Evaluate side-chains 272 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.132730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111206 restraints weight = 13822.636| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.28 r_work: 0.3290 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10041 Z= 0.142 Angle : 0.577 9.033 13616 Z= 0.294 Chirality : 0.044 0.138 1597 Planarity : 0.005 0.053 1723 Dihedral : 4.543 36.013 1342 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 4.61 % Allowed : 25.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.25), residues: 1232 helix: 1.94 (0.22), residues: 595 sheet: 0.29 (0.40), residues: 196 loop : -1.73 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 225 TYR 0.010 0.001 TYR D 322 PHE 0.021 0.001 PHE C 138 TRP 0.009 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00344 (10041) covalent geometry : angle 0.57682 (13616) hydrogen bonds : bond 0.04722 ( 490) hydrogen bonds : angle 4.25938 ( 1404) *********************** 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 283 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8376 (pt0) cc_final: 0.8139 (pt0) REVERT: A 62 LEU cc_start: 0.8032 (mt) cc_final: 0.7704 (mp) REVERT: A 242 LEU cc_start: 0.8087 (mm) cc_final: 0.7870 (mt) REVERT: A 300 ARG cc_start: 0.7212 (mpt180) cc_final: 0.6591 (mpt180) REVERT: B 204 MET cc_start: 0.7959 (tpp) cc_final: 0.7494 (tpp) REVERT: B 270 VAL cc_start: 0.7844 (t) cc_final: 0.7624 (t) REVERT: C 99 MET cc_start: 0.7145 (tpt) cc_final: 0.6195 (mtp) REVERT: C 182 MET cc_start: 0.7226 (tpp) cc_final: 0.6965 (tpp) REVERT: D 38 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8131 (tp) REVERT: D 76 LEU cc_start: 0.7511 (mp) cc_final: 0.7261 (mt) REVERT: D 227 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7767 (mm-30) REVERT: D 260 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5764 (pm20) REVERT: D 277 ASN cc_start: 0.8182 (p0) cc_final: 0.7883 (p0) REVERT: D 323 LYS cc_start: 0.8502 (mttp) cc_final: 0.8177 (mttp) outliers start: 50 outliers final: 41 residues processed: 263 average time/residue: 0.1001 time to fit residues: 36.1691 Evaluate side-chains 274 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 175 LYS 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 260 GLU Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 349 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110525 restraints weight = 13743.337| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.26 r_work: 0.3281 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10041 Z= 0.168 Angle : 0.597 9.394 13616 Z= 0.304 Chirality : 0.045 0.140 1597 Planarity : 0.005 0.054 1723 Dihedral : 4.583 35.963 1342 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 5.07 % Allowed : 25.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.25), residues: 1232 helix: 1.87 (0.22), residues: 595 sheet: 0.28 (0.40), residues: 194 loop : -1.74 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 274 TYR 0.011 0.001 TYR D 322 PHE 0.023 0.001 PHE C 138 TRP 0.010 0.001 TRP A 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00416 (10041) covalent geometry : angle 0.59653 (13616) hydrogen bonds : bond 0.05070 ( 490) hydrogen bonds : angle 4.29625 ( 1404) *********************** 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 282 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8405 (pt0) cc_final: 0.8133 (pt0) REVERT: A 62 LEU cc_start: 0.8036 (mt) cc_final: 0.7695 (mp) REVERT: A 242 LEU cc_start: 0.8086 (mm) cc_final: 0.7873 (mt) REVERT: A 300 ARG cc_start: 0.7224 (mpt180) cc_final: 0.6623 (mpt180) REVERT: C 65 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8076 (p) REVERT: C 99 MET cc_start: 0.7318 (tpt) cc_final: 0.6358 (mtm) REVERT: C 178 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7371 (mp) REVERT: C 182 MET cc_start: 0.7253 (tpp) cc_final: 0.6875 (mpp) REVERT: C 244 MET cc_start: 0.6839 (ttm) cc_final: 0.6614 (ttm) REVERT: D 38 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8146 (tp) REVERT: D 260 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5787 (pm20) REVERT: D 277 ASN cc_start: 0.8209 (p0) cc_final: 0.7878 (p0) REVERT: D 323 LYS cc_start: 0.8519 (mttp) cc_final: 0.8193 (mttp) REVERT: D 353 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5581 (m-30) outliers start: 55 outliers final: 40 residues processed: 262 average time/residue: 0.0939 time to fit residues: 34.3045 Evaluate side-chains 271 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 65 THR 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 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 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 200 THR 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 278 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 349 ASP 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 88 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.132468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111156 restraints weight = 13744.992| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.25 r_work: 0.3290 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10041 Z= 0.148 Angle : 0.599 9.050 13616 Z= 0.301 Chirality : 0.044 0.150 1597 Planarity : 0.005 0.056 1723 Dihedral : 4.369 36.506 1339 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 4.79 % Allowed : 25.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1232 helix: 1.93 (0.22), residues: 594 sheet: 0.21 (0.40), residues: 196 loop : -1.78 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 274 TYR 0.010 0.001 TYR D 322 PHE 0.021 0.001 PHE C 138 TRP 0.008 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00365 (10041) covalent geometry : angle 0.59858 (13616) hydrogen bonds : bond 0.04705 ( 490) hydrogen bonds : angle 4.25539 ( 1404) *********************** 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 270 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.363 Fit side-chains REVERT: A 44 GLU cc_start: 0.8379 (pt0) cc_final: 0.8093 (pt0) REVERT: A 62 LEU cc_start: 0.8040 (mt) cc_final: 0.7710 (mp) REVERT: A 242 LEU cc_start: 0.8077 (mm) cc_final: 0.7860 (mt) REVERT: A 300 ARG cc_start: 0.7209 (mpt180) cc_final: 0.6596 (mpt180) REVERT: B 204 MET cc_start: 0.7928 (tpp) cc_final: 0.7482 (tpp) REVERT: C 99 MET cc_start: 0.7291 (tpt) cc_final: 0.6326 (mtm) REVERT: C 182 MET cc_start: 0.7223 (tpp) cc_final: 0.6797 (mpp) REVERT: C 244 MET cc_start: 0.6807 (ttm) cc_final: 0.6579 (ttm) REVERT: D 38 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8137 (tp) REVERT: D 260 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5803 (pm20) REVERT: D 277 ASN cc_start: 0.8214 (p0) cc_final: 0.7883 (p0) REVERT: D 323 LYS cc_start: 0.8495 (mttp) cc_final: 0.8197 (mttp) REVERT: D 353 ASP cc_start: 0.5747 (OUTLIER) cc_final: 0.5409 (m-30) outliers start: 52 outliers final: 40 residues processed: 253 average time/residue: 0.0967 time to fit residues: 34.1910 Evaluate side-chains 262 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LYS 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 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 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 235 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.132883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111470 restraints weight = 13727.131| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.26 r_work: 0.3298 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10041 Z= 0.138 Angle : 0.589 8.805 13616 Z= 0.296 Chirality : 0.044 0.139 1597 Planarity : 0.005 0.056 1723 Dihedral : 4.312 37.038 1339 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.25), residues: 1232 helix: 1.97 (0.22), residues: 594 sheet: 0.22 (0.40), residues: 196 loop : -1.74 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 274 TYR 0.010 0.001 TYR D 322 PHE 0.020 0.001 PHE C 138 TRP 0.009 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00335 (10041) covalent geometry : angle 0.58871 (13616) hydrogen bonds : bond 0.04496 ( 490) hydrogen bonds : angle 4.19181 ( 1404) *********************** 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 260 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8381 (pt0) cc_final: 0.8100 (pt0) REVERT: A 62 LEU cc_start: 0.8031 (mt) cc_final: 0.7703 (mp) REVERT: A 242 LEU cc_start: 0.8069 (mm) cc_final: 0.7853 (mt) REVERT: A 300 ARG cc_start: 0.7210 (mpt180) cc_final: 0.6595 (mpt180) REVERT: A 360 MET cc_start: 0.4942 (mpp) cc_final: 0.4628 (mpp) REVERT: B 204 MET cc_start: 0.7913 (tpp) cc_final: 0.7454 (tpp) REVERT: B 270 VAL cc_start: 0.7841 (t) cc_final: 0.7607 (t) REVERT: C 65 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8082 (p) REVERT: C 99 MET cc_start: 0.7378 (tpt) cc_final: 0.6435 (mtm) REVERT: C 178 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7257 (mp) REVERT: C 182 MET cc_start: 0.7210 (tpp) cc_final: 0.6939 (tpp) REVERT: C 244 MET cc_start: 0.6787 (ttm) cc_final: 0.6564 (ttm) REVERT: D 38 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8132 (tp) REVERT: D 260 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5781 (pm20) REVERT: D 323 LYS cc_start: 0.8488 (mttp) cc_final: 0.8198 (mttp) REVERT: D 353 ASP cc_start: 0.5561 (OUTLIER) cc_final: 0.5284 (m-30) outliers start: 49 outliers final: 38 residues processed: 245 average time/residue: 0.0920 time to fit residues: 31.4829 Evaluate side-chains 254 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LYS 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 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 169 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.134794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113463 restraints weight = 13593.094| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.26 r_work: 0.3326 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10041 Z= 0.114 Angle : 0.574 8.550 13616 Z= 0.286 Chirality : 0.043 0.134 1597 Planarity : 0.005 0.057 1723 Dihedral : 4.181 37.854 1339 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 3.13 % Allowed : 27.74 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.25), residues: 1232 helix: 2.04 (0.22), residues: 596 sheet: 0.23 (0.40), residues: 196 loop : -1.68 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.009 0.001 TYR D 322 PHE 0.018 0.001 PHE C 138 TRP 0.011 0.001 TRP D 364 HIS 0.009 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00264 (10041) covalent geometry : angle 0.57350 (13616) hydrogen bonds : bond 0.03904 ( 490) hydrogen bonds : angle 4.09954 ( 1404) ********************** 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 248 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8336 (pt0) cc_final: 0.8031 (pt0) REVERT: A 62 LEU cc_start: 0.8075 (mt) cc_final: 0.7752 (mp) REVERT: A 241 ASN cc_start: 0.8358 (p0) cc_final: 0.7983 (p0) REVERT: A 242 LEU cc_start: 0.8086 (mm) cc_final: 0.7873 (mt) REVERT: A 300 ARG cc_start: 0.7189 (mpt180) cc_final: 0.6594 (mpt180) REVERT: A 360 MET cc_start: 0.4902 (mpp) cc_final: 0.4573 (mpp) REVERT: B 204 MET cc_start: 0.7833 (tpp) cc_final: 0.7468 (tpp) REVERT: B 270 VAL cc_start: 0.7909 (t) cc_final: 0.7658 (t) REVERT: C 99 MET cc_start: 0.7402 (tpt) cc_final: 0.6487 (mtm) REVERT: C 182 MET cc_start: 0.7126 (tpp) cc_final: 0.6887 (tpp) REVERT: C 244 MET cc_start: 0.6809 (ttm) cc_final: 0.6578 (ttm) REVERT: D 38 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8154 (tp) REVERT: D 260 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5690 (pm20) REVERT: D 323 LYS cc_start: 0.8479 (mttp) cc_final: 0.8188 (mttp) REVERT: D 353 ASP cc_start: 0.5367 (OUTLIER) cc_final: 0.5129 (m-30) outliers start: 34 outliers final: 29 residues processed: 237 average time/residue: 0.0981 time to fit residues: 32.2150 Evaluate side-chains 246 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 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 60 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.134731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113612 restraints weight = 13621.995| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.21 r_work: 0.3315 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.051 10041 Z= 0.136 Angle : 0.594 8.536 13616 Z= 0.296 Chirality : 0.044 0.192 1597 Planarity : 0.006 0.057 1723 Dihedral : 4.212 37.759 1339 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 3.59 % Allowed : 27.28 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.25), residues: 1232 helix: 1.99 (0.22), residues: 597 sheet: 0.33 (0.40), residues: 194 loop : -1.64 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 233 TYR 0.009 0.001 TYR D 322 PHE 0.020 0.001 PHE C 138 TRP 0.009 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00333 (10041) covalent geometry : angle 0.59384 (13616) hydrogen bonds : bond 0.04359 ( 490) hydrogen bonds : angle 4.12330 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.47 seconds wall clock time: 46 minutes 31.38 seconds (2791.38 seconds total)