Starting phenix.real_space_refine on Sat Aug 23 02:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6n_36924/08_2025/8k6n_36924.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6n_36924/08_2025/8k6n_36924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k6n_36924/08_2025/8k6n_36924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6n_36924/08_2025/8k6n_36924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k6n_36924/08_2025/8k6n_36924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6n_36924/08_2025/8k6n_36924.map" } resolution = 3.2 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= 0.002 sd= 0.029 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 5915 2.51 5 N 1575 2.21 5 O 1741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9291 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1807 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 267 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain breaks: 1 Chain: "E" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2387 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 10, 'TRANS': 290} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 1.81, per 1000 atoms: 0.19 Number of scatterers: 9291 At special positions: 0 Unit cell: (136, 123.25, 105.4, 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 1741 8.00 N 1575 7.00 C 5915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 123 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.61 Conformation dependent library (CDL) restraints added in 239.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 37.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.778A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.589A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.984A pdb=" N LYS A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.960A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.674A pdb=" N GLN A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.964A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 16 through 32 Processing helix chain 'E' and resid 46 through 78 removed outlier: 3.786A pdb=" N PHE E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 114 removed outlier: 4.183A pdb=" N LEU E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Proline residue: E 105 - end of helix Processing helix chain 'E' and resid 119 through 153 Proline residue: E 127 - end of helix Processing helix chain 'E' and resid 161 through 180 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.237A pdb=" N ALA E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 228 removed outlier: 4.520A pdb=" N THR E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 248 Processing helix chain 'E' and resid 256 through 281 removed outlier: 3.976A pdb=" N HIS E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 261 " --> pdb=" O ASP E 257 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS E 265 " --> pdb=" O GLN E 261 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 292 removed outlier: 3.994A pdb=" N HIS E 285 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 316 Processing helix chain 'E' and resid 316 through 327 Proline residue: E 322 - end of helix Processing helix chain 'E' and resid 329 through 339 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.850A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.154A pdb=" N MET A 241 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.844A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.663A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.394A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.536A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.866A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.235A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.885A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 288 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 188 through 194 removed outlier: 4.060A pdb=" N GLU E 188 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 204 " --> pdb=" O GLU E 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.612A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 71 through 73 Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB6, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.860A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER S 208 " --> pdb=" O ALA S 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.824A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1293 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: 0.94 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2716 1.33 - 1.46: 2118 1.46 - 1.58: 4561 1.58 - 1.70: 1 1.70 - 1.83: 88 Bond restraints: 9484 Sorted by residual: bond pdb=" CA SER D 22 " pdb=" CB SER D 22 " ideal model delta sigma weight residual 1.529 1.488 0.041 1.55e-02 4.16e+03 6.89e+00 bond pdb=" N SER D 3 " pdb=" CA SER D 3 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.69e+00 bond pdb=" CA SER D 3 " pdb=" CB SER D 3 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.50e-02 4.44e+03 6.20e+00 bond pdb=" CB PRO C 60 " pdb=" CG PRO C 60 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.42e+00 bond pdb=" N LYS D 4 " pdb=" CA LYS D 4 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.45e-02 4.76e+03 5.34e+00 ... (remaining 9479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 12389 1.56 - 3.12: 363 3.12 - 4.68: 68 4.68 - 6.24: 22 6.24 - 7.80: 5 Bond angle restraints: 12847 Sorted by residual: angle pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" CD PRO C 60 " ideal model delta sigma weight residual 112.00 104.94 7.06 1.40e+00 5.10e-01 2.54e+01 angle pdb=" C LYS E 268 " pdb=" N MET E 269 " pdb=" CA MET E 269 " ideal model delta sigma weight residual 121.14 113.34 7.80 1.75e+00 3.27e-01 1.99e+01 angle pdb=" N ILE D 28 " pdb=" CA ILE D 28 " pdb=" C ILE D 28 " ideal model delta sigma weight residual 110.62 106.62 4.00 1.02e+00 9.61e-01 1.54e+01 angle pdb=" CA ASN D 29 " pdb=" C ASN D 29 " pdb=" O ASN D 29 " ideal model delta sigma weight residual 120.82 116.92 3.90 1.05e+00 9.07e-01 1.38e+01 angle pdb=" CA ARG D 35 " pdb=" C ARG D 35 " pdb=" O ARG D 35 " ideal model delta sigma weight residual 120.70 116.90 3.80 1.08e+00 8.57e-01 1.24e+01 ... (remaining 12842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5107 17.31 - 34.62: 440 34.62 - 51.94: 80 51.94 - 69.25: 9 69.25 - 86.56: 6 Dihedral angle restraints: 5642 sinusoidal: 2195 harmonic: 3447 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 60.52 32.48 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA PHE A 268 " pdb=" C PHE A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLY S 26 " pdb=" C GLY S 26 " pdb=" N PHE S 27 " pdb=" CA PHE S 27 " ideal model delta harmonic sigma weight residual 180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1248 0.063 - 0.126: 194 0.126 - 0.189: 14 0.189 - 0.252: 8 0.252 - 0.316: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA TYR D 27 " pdb=" N TYR D 27 " pdb=" C TYR D 27 " pdb=" CB TYR D 27 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ARG D 35 " pdb=" N ARG D 35 " pdb=" C ARG D 35 " pdb=" CB ARG D 35 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1463 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " 0.033 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 60 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " -0.012 2.00e-02 2.50e+03 1.14e-02 3.22e+00 pdb=" CG TRP S 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 251 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO E 252 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 252 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 252 " -0.024 5.00e-02 4.00e+02 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1038 2.75 - 3.29: 9080 3.29 - 3.82: 14961 3.82 - 4.36: 16897 4.36 - 4.90: 29865 Nonbonded interactions: 71841 Sorted by model distance: nonbonded pdb=" NH1 ARG E 263 " pdb=" OG1 THR E 266 " model vdw 2.211 3.120 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.216 3.040 nonbonded pdb=" O CYS A 255 " pdb=" NZ LYS A 318 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR E 44 " pdb=" O LYS E 301 " model vdw 2.237 3.040 nonbonded pdb=" NE ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.238 3.120 ... (remaining 71836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 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 : 0.004 0.116 9486 Z= 0.204 Angle : 0.663 7.797 12851 Z= 0.384 Chirality : 0.048 0.316 1466 Planarity : 0.004 0.048 1618 Dihedral : 13.234 86.559 3412 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.10 % Allowed : 0.79 % Favored : 99.12 % 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: 0.15 (0.25), residues: 1168 helix: 1.96 (0.26), residues: 408 sheet: -0.15 (0.32), residues: 273 loop : -1.39 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 33 TYR 0.027 0.002 TYR D 27 PHE 0.018 0.002 PHE B 235 TRP 0.031 0.002 TRP S 111 HIS 0.007 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9484) covalent geometry : angle 0.66222 (12847) SS BOND : bond 0.00684 ( 2) SS BOND : angle 2.31912 ( 4) hydrogen bonds : bond 0.15379 ( 444) hydrogen bonds : angle 6.22289 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.336 Fit side-chains REVERT: A 262 ASP cc_start: 0.6790 (t0) cc_final: 0.6548 (t0) REVERT: B 66 ASP cc_start: 0.8367 (p0) cc_final: 0.7777 (p0) REVERT: E 107 THR cc_start: 0.8108 (m) cc_final: 0.7899 (m) REVERT: E 226 ILE cc_start: 0.8028 (tp) cc_final: 0.7760 (tp) REVERT: E 248 ASN cc_start: 0.6941 (m-40) cc_final: 0.6582 (m-40) REVERT: E 267 THR cc_start: 0.7508 (m) cc_final: 0.7307 (m) outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.0835 time to fit residues: 18.7537 Evaluate side-chains 154 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN E 329 ASN S 142 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.174559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143794 restraints weight = 13123.974| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.47 r_work: 0.3740 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9486 Z= 0.133 Angle : 0.595 10.224 12851 Z= 0.308 Chirality : 0.042 0.152 1466 Planarity : 0.004 0.038 1618 Dihedral : 5.016 86.413 1284 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.57 % Allowed : 9.32 % Favored : 89.11 % 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: 0.32 (0.25), residues: 1168 helix: 2.18 (0.26), residues: 419 sheet: -0.19 (0.31), residues: 278 loop : -1.39 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 38 TYR 0.026 0.002 TYR D 27 PHE 0.014 0.002 PHE E 319 TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9484) covalent geometry : angle 0.59369 (12847) SS BOND : bond 0.00538 ( 2) SS BOND : angle 2.03721 ( 4) hydrogen bonds : bond 0.05516 ( 444) hydrogen bonds : angle 4.94915 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5804 (mp) cc_final: 0.5537 (mp) REVERT: A 262 ASP cc_start: 0.7241 (t0) cc_final: 0.6993 (t0) REVERT: A 341 THR cc_start: 0.8042 (m) cc_final: 0.7836 (m) REVERT: B 340 ASN cc_start: 0.7611 (t0) cc_final: 0.7326 (t0) REVERT: C 44 HIS cc_start: 0.8191 (m-70) cc_final: 0.7944 (m90) REVERT: E 226 ILE cc_start: 0.8176 (tp) cc_final: 0.7832 (tp) REVERT: E 248 ASN cc_start: 0.7150 (m-40) cc_final: 0.6803 (m-40) outliers start: 16 outliers final: 11 residues processed: 159 average time/residue: 0.0906 time to fit residues: 19.7960 Evaluate side-chains 164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 26 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.172149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.141380 restraints weight = 13218.548| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.48 r_work: 0.3728 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9486 Z= 0.142 Angle : 0.573 9.338 12851 Z= 0.299 Chirality : 0.042 0.150 1466 Planarity : 0.004 0.038 1618 Dihedral : 4.918 86.526 1281 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.45 % Allowed : 12.86 % Favored : 84.69 % 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: 0.39 (0.25), residues: 1168 helix: 2.31 (0.26), residues: 417 sheet: -0.25 (0.31), residues: 284 loop : -1.35 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 38 TYR 0.021 0.002 TYR D 27 PHE 0.013 0.001 PHE A 190 TRP 0.021 0.002 TRP B 169 HIS 0.008 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9484) covalent geometry : angle 0.57207 (12847) SS BOND : bond 0.00630 ( 2) SS BOND : angle 1.76144 ( 4) hydrogen bonds : bond 0.05485 ( 444) hydrogen bonds : angle 4.79517 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7273 (t0) cc_final: 0.7009 (t0) REVERT: D 32 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7454 (t) REVERT: E 226 ILE cc_start: 0.8216 (tp) cc_final: 0.7857 (tp) REVERT: E 248 ASN cc_start: 0.7205 (m-40) cc_final: 0.6868 (m-40) outliers start: 25 outliers final: 18 residues processed: 165 average time/residue: 0.0690 time to fit residues: 15.9044 Evaluate side-chains 174 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 26 HIS E 256 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.173457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142704 restraints weight = 13212.544| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.47 r_work: 0.3730 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9486 Z= 0.139 Angle : 0.568 7.918 12851 Z= 0.297 Chirality : 0.041 0.149 1466 Planarity : 0.004 0.037 1618 Dihedral : 4.917 87.503 1281 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.55 % Allowed : 14.62 % Favored : 82.83 % 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: 0.40 (0.25), residues: 1168 helix: 2.33 (0.26), residues: 417 sheet: -0.21 (0.31), residues: 283 loop : -1.37 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 38 TYR 0.018 0.002 TYR D 27 PHE 0.013 0.001 PHE A 190 TRP 0.020 0.002 TRP B 169 HIS 0.008 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9484) covalent geometry : angle 0.56674 (12847) SS BOND : bond 0.00586 ( 2) SS BOND : angle 1.77373 ( 4) hydrogen bonds : bond 0.05339 ( 444) hydrogen bonds : angle 4.66974 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7276 (t0) cc_final: 0.6992 (t0) REVERT: D 32 THR cc_start: 0.7710 (OUTLIER) cc_final: 0.7421 (t) REVERT: E 153 VAL cc_start: 0.8186 (p) cc_final: 0.7920 (m) REVERT: E 179 LEU cc_start: 0.7499 (tp) cc_final: 0.7253 (tt) REVERT: E 226 ILE cc_start: 0.8221 (tp) cc_final: 0.7858 (tp) REVERT: E 248 ASN cc_start: 0.7197 (m-40) cc_final: 0.6868 (m-40) outliers start: 26 outliers final: 21 residues processed: 166 average time/residue: 0.0831 time to fit residues: 19.2460 Evaluate side-chains 178 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 0.3980 chunk 94 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 26 HIS E 149 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.174121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143450 restraints weight = 13191.645| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.50 r_work: 0.3749 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9486 Z= 0.114 Angle : 0.559 10.191 12851 Z= 0.289 Chirality : 0.040 0.132 1466 Planarity : 0.004 0.035 1618 Dihedral : 4.811 87.326 1281 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.65 % Allowed : 16.68 % Favored : 80.67 % 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: 0.51 (0.25), residues: 1168 helix: 2.43 (0.26), residues: 417 sheet: -0.20 (0.31), residues: 281 loop : -1.28 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.016 0.001 TYR D 27 PHE 0.013 0.001 PHE E 319 TRP 0.022 0.002 TRP B 332 HIS 0.007 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9484) covalent geometry : angle 0.55862 (12847) SS BOND : bond 0.00571 ( 2) SS BOND : angle 1.47722 ( 4) hydrogen bonds : bond 0.04641 ( 444) hydrogen bonds : angle 4.47367 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5942 (mp) cc_final: 0.5682 (mp) REVERT: A 262 ASP cc_start: 0.7196 (t0) cc_final: 0.6906 (t0) REVERT: C 46 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8640 (mtpt) REVERT: D 32 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7381 (t) REVERT: E 153 VAL cc_start: 0.8168 (p) cc_final: 0.7872 (m) REVERT: E 226 ILE cc_start: 0.8156 (tp) cc_final: 0.7778 (tp) REVERT: E 248 ASN cc_start: 0.7041 (m-40) cc_final: 0.6807 (m-40) REVERT: S 187 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8223 (tp) outliers start: 27 outliers final: 18 residues processed: 162 average time/residue: 0.0680 time to fit residues: 15.8154 Evaluate side-chains 165 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 26 HIS ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.167379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136838 restraints weight = 13213.479| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.43 r_work: 0.3663 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 9486 Z= 0.285 Angle : 0.692 9.203 12851 Z= 0.363 Chirality : 0.047 0.199 1466 Planarity : 0.005 0.039 1618 Dihedral : 5.308 86.546 1281 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.43 % Allowed : 16.78 % Favored : 79.78 % 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: 0.06 (0.25), residues: 1168 helix: 2.05 (0.26), residues: 411 sheet: -0.22 (0.31), residues: 279 loop : -1.65 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.030 0.003 TYR B 105 PHE 0.025 0.003 PHE A 337 TRP 0.032 0.003 TRP B 169 HIS 0.009 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 9484) covalent geometry : angle 0.69056 (12847) SS BOND : bond 0.00962 ( 2) SS BOND : angle 2.48270 ( 4) hydrogen bonds : bond 0.07393 ( 444) hydrogen bonds : angle 4.99326 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.229 Fit side-chains REVERT: A 262 ASP cc_start: 0.7263 (t0) cc_final: 0.6945 (t0) REVERT: B 118 ASP cc_start: 0.8079 (t0) cc_final: 0.7649 (t0) REVERT: B 298 ASP cc_start: 0.7451 (t0) cc_final: 0.7075 (t0) REVERT: E 69 SER cc_start: 0.8223 (m) cc_final: 0.8002 (m) REVERT: E 111 THR cc_start: 0.8621 (t) cc_final: 0.8324 (t) REVERT: E 153 VAL cc_start: 0.8241 (p) cc_final: 0.7935 (m) REVERT: E 226 ILE cc_start: 0.8302 (tp) cc_final: 0.7935 (tp) REVERT: E 248 ASN cc_start: 0.7380 (m-40) cc_final: 0.7032 (m-40) REVERT: E 271 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7788 (p) REVERT: S 140 MET cc_start: 0.5131 (mtp) cc_final: 0.4930 (ttp) outliers start: 35 outliers final: 26 residues processed: 174 average time/residue: 0.0747 time to fit residues: 18.3961 Evaluate side-chains 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 26 HIS D 29 ASN E 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.172240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141458 restraints weight = 13129.676| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.53 r_work: 0.3690 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9486 Z= 0.154 Angle : 0.609 10.657 12851 Z= 0.316 Chirality : 0.042 0.142 1466 Planarity : 0.004 0.048 1618 Dihedral : 5.044 85.047 1281 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 18.35 % Favored : 78.61 % 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: 0.23 (0.25), residues: 1168 helix: 2.25 (0.26), residues: 411 sheet: -0.28 (0.31), residues: 268 loop : -1.46 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.018 0.002 TYR B 105 PHE 0.015 0.002 PHE B 235 TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9484) covalent geometry : angle 0.60822 (12847) SS BOND : bond 0.00779 ( 2) SS BOND : angle 1.83212 ( 4) hydrogen bonds : bond 0.05751 ( 444) hydrogen bonds : angle 4.66767 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7240 (t0) cc_final: 0.6916 (t0) REVERT: B 298 ASP cc_start: 0.7441 (t0) cc_final: 0.7098 (t0) REVERT: D 32 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7497 (t) REVERT: E 69 SER cc_start: 0.8155 (m) cc_final: 0.7954 (m) REVERT: E 153 VAL cc_start: 0.8217 (p) cc_final: 0.7922 (m) REVERT: E 226 ILE cc_start: 0.8213 (tp) cc_final: 0.7840 (tp) REVERT: E 248 ASN cc_start: 0.7233 (m-40) cc_final: 0.6905 (m-40) REVERT: E 271 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7825 (p) outliers start: 31 outliers final: 24 residues processed: 169 average time/residue: 0.0717 time to fit residues: 16.8520 Evaluate side-chains 179 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 26 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142442 restraints weight = 13072.749| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.50 r_work: 0.3713 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9486 Z= 0.127 Angle : 0.600 10.784 12851 Z= 0.308 Chirality : 0.041 0.168 1466 Planarity : 0.004 0.039 1618 Dihedral : 4.918 84.237 1281 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.55 % Allowed : 19.23 % Favored : 78.21 % 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: 0.36 (0.25), residues: 1168 helix: 2.34 (0.26), residues: 411 sheet: -0.26 (0.31), residues: 277 loop : -1.36 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.014 0.001 TYR S 102 PHE 0.012 0.001 PHE A 190 TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9484) covalent geometry : angle 0.59922 (12847) SS BOND : bond 0.00821 ( 2) SS BOND : angle 1.99974 ( 4) hydrogen bonds : bond 0.05069 ( 444) hydrogen bonds : angle 4.51748 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7109 (mpt) cc_final: 0.6818 (mpt) REVERT: A 262 ASP cc_start: 0.7209 (t0) cc_final: 0.6896 (t0) REVERT: B 298 ASP cc_start: 0.7357 (t0) cc_final: 0.7000 (t0) REVERT: C 46 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8676 (mtpt) REVERT: D 32 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7492 (t) REVERT: E 69 SER cc_start: 0.8114 (m) cc_final: 0.7906 (m) REVERT: E 153 VAL cc_start: 0.8228 (p) cc_final: 0.7912 (m) REVERT: E 226 ILE cc_start: 0.8171 (tp) cc_final: 0.7788 (tp) REVERT: E 248 ASN cc_start: 0.7092 (m-40) cc_final: 0.6867 (m-40) REVERT: E 271 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7808 (p) REVERT: E 329 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8110 (m-40) REVERT: S 140 MET cc_start: 0.5040 (mtp) cc_final: 0.4826 (ttp) outliers start: 26 outliers final: 19 residues processed: 173 average time/residue: 0.0793 time to fit residues: 18.9586 Evaluate side-chains 180 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.173497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142849 restraints weight = 13010.121| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.47 r_work: 0.3711 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9486 Z= 0.144 Angle : 0.621 11.354 12851 Z= 0.317 Chirality : 0.042 0.138 1466 Planarity : 0.004 0.039 1618 Dihedral : 4.878 82.263 1281 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 19.53 % Favored : 77.43 % 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: 0.32 (0.25), residues: 1168 helix: 2.33 (0.26), residues: 411 sheet: -0.25 (0.32), residues: 270 loop : -1.42 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.018 0.002 TYR B 105 PHE 0.016 0.001 PHE B 235 TRP 0.018 0.002 TRP B 169 HIS 0.007 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9484) covalent geometry : angle 0.61984 (12847) SS BOND : bond 0.00853 ( 2) SS BOND : angle 1.95060 ( 4) hydrogen bonds : bond 0.05315 ( 444) hydrogen bonds : angle 4.52612 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7240 (t0) cc_final: 0.6918 (t0) REVERT: B 118 ASP cc_start: 0.8020 (t0) cc_final: 0.7681 (t0) REVERT: B 298 ASP cc_start: 0.7360 (t0) cc_final: 0.6994 (t0) REVERT: D 32 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7491 (t) REVERT: E 69 SER cc_start: 0.8122 (m) cc_final: 0.7914 (m) REVERT: E 153 VAL cc_start: 0.8168 (p) cc_final: 0.7844 (m) REVERT: E 210 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: E 226 ILE cc_start: 0.8203 (tp) cc_final: 0.7819 (tp) REVERT: E 248 ASN cc_start: 0.7039 (m-40) cc_final: 0.6807 (m-40) REVERT: E 271 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7783 (p) REVERT: E 329 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8154 (m-40) REVERT: S 140 MET cc_start: 0.4969 (mtp) cc_final: 0.4736 (ttp) outliers start: 31 outliers final: 24 residues processed: 169 average time/residue: 0.0717 time to fit residues: 17.0528 Evaluate side-chains 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 70 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 0.0070 chunk 108 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.174359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.143445 restraints weight = 13147.202| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.54 r_work: 0.3726 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9486 Z= 0.131 Angle : 0.623 12.241 12851 Z= 0.317 Chirality : 0.041 0.160 1466 Planarity : 0.004 0.036 1618 Dihedral : 4.808 81.292 1281 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.85 % Allowed : 19.73 % Favored : 77.43 % 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: 0.39 (0.25), residues: 1168 helix: 2.33 (0.26), residues: 411 sheet: -0.19 (0.31), residues: 281 loop : -1.34 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.015 0.001 TYR B 105 PHE 0.013 0.001 PHE B 235 TRP 0.049 0.002 TRP B 332 HIS 0.005 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9484) covalent geometry : angle 0.62280 (12847) SS BOND : bond 0.00783 ( 2) SS BOND : angle 1.76109 ( 4) hydrogen bonds : bond 0.04976 ( 444) hydrogen bonds : angle 4.48575 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7137 (t0) cc_final: 0.6822 (t0) REVERT: B 298 ASP cc_start: 0.7343 (t0) cc_final: 0.7002 (t0) REVERT: D 32 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7500 (t) REVERT: E 153 VAL cc_start: 0.8179 (p) cc_final: 0.7864 (m) REVERT: E 179 LEU cc_start: 0.7008 (tt) cc_final: 0.6540 (tt) REVERT: E 226 ILE cc_start: 0.8168 (tp) cc_final: 0.7785 (tp) REVERT: E 271 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7794 (p) REVERT: E 329 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8204 (m-40) outliers start: 29 outliers final: 24 residues processed: 168 average time/residue: 0.0680 time to fit residues: 16.2334 Evaluate side-chains 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.0370 chunk 56 optimal weight: 5.9990 chunk 24 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145515 restraints weight = 13080.857| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.52 r_work: 0.3762 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9486 Z= 0.111 Angle : 0.604 11.755 12851 Z= 0.305 Chirality : 0.041 0.163 1466 Planarity : 0.004 0.035 1618 Dihedral : 4.665 80.919 1281 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.45 % Allowed : 20.31 % Favored : 77.23 % 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: 0.44 (0.26), residues: 1168 helix: 2.37 (0.26), residues: 411 sheet: -0.26 (0.31), residues: 288 loop : -1.26 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.013 0.001 TYR S 102 PHE 0.010 0.001 PHE E 319 TRP 0.038 0.002 TRP B 332 HIS 0.004 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9484) covalent geometry : angle 0.60363 (12847) SS BOND : bond 0.00706 ( 2) SS BOND : angle 1.54032 ( 4) hydrogen bonds : bond 0.04090 ( 444) hydrogen bonds : angle 4.29934 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3202.87 seconds wall clock time: 55 minutes 8.47 seconds (3308.47 seconds total)